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Sample records for single-nucleotide ber sub-pathway

  1. Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase

    Science.gov (United States)

    Wang, Quan; Serban, Andrew J.; Wachter, Rebekka M.; Moerner, W. E.

    2018-03-01

    Oligomerization plays an important role in the function of many proteins, but a quantitative picture of the oligomer distribution has been difficult to obtain using existing techniques. Here we describe a method that combines sub-stoichiometric labeling and recently developed single-molecule diffusometry to measure the size distribution of oligomers under equilibrium conditions in solution, one molecule at a time. We use this technique to characterize the oligomerization behavior of Nicotiana tabacum (Nt) Rubisco activase (Nt-Rca), a chaperone-like AAA-plus ATPase essential in regulating carbon fixation during photosynthesis. We directly observed monomers, dimers, and a tetramer/hexamer mixture and extracted their fractional abundance as a function of protein concentration. We show that the oligomerization pathway of Nt-Rca is nucleotide dependent: ATPγS binding strongly promotes tetramer/hexamer formation from dimers and results in a preferred tetramer/hexamer population for concentrations in the 1-10 μM range. Furthermore, we directly observed dynamic assembly and disassembly processes of single complexes in real time and from there estimated the rate of subunit exchange to be ˜0.1 s-1 with ATPγS. On the other hand, ADP binding destabilizes Rca complexes by enhancing the rate of subunit exchange by >2 fold. These observations provide a quantitative starting point to elucidate the structure-function relations of Nt-Rca complexes. We envision the method to fill a critical gap in defining and quantifying protein assembly pathways in the small-oligomer regime.

  2. Coupling of the nucleotide incision and 3' {yields} 5' exonuclease activities in Escherichia coli endonuclease IV: Structural and genetic evidences

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    Golan, Gali [Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Ishchenko, Alexander A. [Groupe Reparation de l' ADN, CNRS UMR 8126, Univ. Paris-Sud, Institut de Cancerologie Gustave Roussy, 39, rue Camille Desmoulins, F-94805 Villejuif Cedex (France); Khassenov, Bekbolat [National Center for Biotechnology, Astana (Kazakhstan); Shoham, Gil, E-mail: gil2@vms.huji.ac.il [Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Saparbaev, Murat K., E-mail: smurat@igr.fr [Groupe Reparation de l' ADN, CNRS UMR 8126, Univ. Paris-Sud, Institut de Cancerologie Gustave Roussy, 39, rue Camille Desmoulins, F-94805 Villejuif Cedex (France)

    2010-03-01

    Aerobic respiration generates reactive oxygen species (ROS) as a by-product of cellular metabolism which can damage DNA. The complex nature of oxidative DNA damage requires actions of several repair pathways. Oxidized DNA bases are substrates for two overlapping pathways: base excision repair (BER) and nucleotide incision repair (NIR). In the BER pathway a DNA glycosylase cleaves the N-glycosylic bond between the abnormal base and deoxyribose, leaving either an abasic site or single-stranded DNA break. Alternatively, in the NIR pathway, an apurinic/apyrimidinic (AP) endonuclease incises duplex DNA 5' next to oxidatively damaged nucleotide. The multifunctional Escherichia coli endonuclease IV (Nfo) is involved in both BER and NIR pathways. Nfo incises duplex DNA 5' of a damaged residue but also possesses an intrinsic 3' {yields} 5' exonuclease activity. Herein, we demonstrate that Nfo-catalyzed NIR and exonuclease activities can generate a single-strand gap at the 5' side of 5,6-dihydrouracil residue. Furthermore, we show that Nfo mutants carrying amino acid substitutions H69A and G149D are deficient in both NIR and exonuclease activities, suggesting that these two functions are genetically linked and governed by the same amino acid residues. The crystal structure of Nfo-H69A mutant reveals the loss of one of the active site zinc atoms (Zn1) and rearrangements of the catalytic site, but no gross changes in the overall enzyme conformation. We hypothesize that these minor changes strongly affect the DNA binding of Nfo. Decreased affinity may lead to a different kinking angle of the DNA helix and this in turn thwart nucleotide incision and exonuclease activities of Nfo mutants but to lesser extent of their AP endonuclease function. Based on the biochemical and genetic data we propose a model where nucleotide incision coupled to 3' {yields} 5' exonuclease activity prevents formation of lethal double-strand breaks when repairing bi

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

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    Modesto Redrejo-Rodríguez

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

  4. Detecting Single-Nucleotides by Tunneling Current Measurements at Sub-MHz Temporal Resolution.

    Science.gov (United States)

    Morikawa, Takanori; Yokota, Kazumichi; Tanimoto, Sachie; Tsutsui, Makusu; Taniguchi, Masateru

    2017-04-18

    Label-free detection of single-nucleotides was performed by fast tunneling current measurements in a polar solvent at 1 MHz sampling rate using SiO₂-protected Au nanoprobes. Short current spikes were observed, suggestive of trapping/detrapping of individual nucleotides between the nanoelectrodes. The fall and rise features of the electrical signatures indicated signal retardation by capacitance effects with a time constant of about 10 microseconds. The high temporal resolution revealed current fluctuations, reflecting the molecular conformation degrees of freedom in the electrode gap. The method presented in this work may enable direct characterizations of dynamic changes in single-molecule conformations in an electrode gap in liquid.

  5. Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication.

    Science.gov (United States)

    Bj Rås, Karine Ø; Sousa, Mirta M L; Sharma, Animesh; Fonseca, Davi M; S Gaard, Caroline K; Bj Rås, Magnar; Otterlei, Marit

    2017-08-21

    Base lesions in DNA can stall the replication machinery or induce mutations if bypassed. Consequently, lesions must be repaired before replication or in a post-replicative process to maintain genomic stability. Base excision repair (BER) is the main pathway for repair of base lesions and is known to be associated with DNA replication, but how BER is organized during replication is unclear. Here we coupled the iPOND (isolation of proteins on nascent DNA) technique with targeted mass-spectrometry analysis, which enabled us to detect all proteins required for BER on nascent DNA and to monitor their spatiotemporal orchestration at replication forks. We demonstrate that XRCC1 and other BER/single-strand break repair (SSBR) proteins are enriched in replisomes in unstressed cells, supporting a cellular capacity of post-replicative BER/SSBR. Importantly, we identify for the first time the DNA glycosylases MYH, UNG2, MPG, NTH1, NEIL1, 2 and 3 on nascent DNA. Our findings suggest that a broad spectrum of DNA base lesions are recognized and repaired by BER in a post-replicative process. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. The low-dose combination preparation Vertigoheel activates cyclic nucleotide pathways and stimulates vasorelaxation.

    Science.gov (United States)

    Heinle, H; Tober, C; Zhang, D; Jäggi, R; Kuebler, W M

    2010-01-01

    Vertigo of various and often unknown aetiologies has been associated with and attributed to impaired microvascular perfusion in the inner ear or the vertebrobasilar system. Vertigoheel is a low-dose combination preparation of proven value in the symptomatic treatment of vertigo. In the present study we tested the hypothesis that Vertigoheel's anti-vertiginous properties may in part be due to a vasodilatory effect exerted via stimulation of the adenylate and/or guanylate cyclase pathways. Thus, the influence of Vertigoheel or its single constituents on synthesis and degradation of cyclic nucleotides was measured. Furthermore, vessel myography was used to observe the effect of Vertigoheel on the vasoreactivity of rat carotid arteries. Vertigoheel and one of its constituents, Anamirta cocculus, stimulated adenylate cyclase activity, while another constituent, Conium maculatum, inhibited phosphodiesterase 5, suggesting that the individual constituents of Vertigoheel contribute differentially to a synergistic stimulation of cyclic nucleotide signalling pathways. In rat carotid artery rings, Vertigoheel counteracted phenylephrine-induced tonic vasoconstriction. The present data demonstrate a vasorelaxant effect of Vertigoheel that goes along with a synergistic stimulation of cyclic nucleotide pathways and may provide a mechanistic basis for the documented anti-vertiginous effects of this combination preparation.

  7. Association Study between Folate Pathway Gene Single Nucleotide Polymorphisms and Gastric Cancer in Koreans

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    Jae-Young Yoo

    2012-09-01

    Full Text Available Gastric cancer is ranked as the most common cancer in Koreans. A recent molecular biological study about the folate pathway gene revealed the correlation with a couple of cancer types. In the folate pathway, several genes are involved, including methylenetetrahydrofolate reductase (MTHFR, methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR, and methyltetrahydrofolate-homocysteine methyltransferase (MTR. The MTHFR gene has been reported several times for the correlation with gastric cancer risk. However, the association of the MTRR or MTR gene has not been reported to date. In this study, we investigated the association between the single nucleotide polymorphisms (SNPs of the MTHFR, MTRR, and MTR genes and the risk of gastric cancer in Koreans. To identify the genetic association with gastric cancer, we selected 17 SNPs sites in folate pathway-associated genes of MTHFR, MTR, and MTRR and tested in 1,261 gastric cancer patients and 375 healthy controls. By genotype analysis, estimating odds ratios and 95% confidence intervals (CI, rs1801394 in the MTRR gene showed increased risk for gastric cacner, with statistical significance both in the codominant model (odds ratio [OR], 1.39; 95% CI, 1.04 to 1.85 and dominant model (OR, 1.34; 95% CI, 1.02 to 1.75. Especially, in the obese group (body mass index ≥ 25 kg/m2, the codominant (OR, 9.08; 95% CI, 1.01 to 94.59 and recessive model (OR, 3.72; 95% CI, 0.92 to 16.59 showed dramatically increased risk (p < 0.05. In conclusion, rs1801394 in the MTRR gene is associated with gastric cancer risk, and its functional significance need to be validated.

  8. The sensitivity of bit error rate (BER) performance in multi-carrier (OFDM) and single-carrier

    Science.gov (United States)

    Albdran, Saleh; Alshammari, Ahmed; Matin, Mohammad

    2012-10-01

    Recently, the single-carrier and multi-carrier transmissions have grabbed the attention of industrial systems. Theoretically, OFDM as a Multicarrier has more advantages over the Single-Carrier especially for high data rate. In this paper we will show which one of the two techniques outperforms the other. We will study and compare the performance of BER for both techniques for a given channel. As a function of signal to noise ratio SNR, the BER will be measure and studied. Also, Peak-to-Average Power Ratio (PAPR) is going to be examined and presented as a drawback of using OFDM. To make a reasonable comparison between the both techniques, we will use additive white Gaussian noise (AWGN) as a communication channel.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-15

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

  10. Single Nucleotide Polymorphism

    DEFF Research Database (Denmark)

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

    2014-01-01

    Single nucleotide polymorphisms (SNPs) are the most frequent DNA sequence variations in the genome. They have been studied extensively in the last decade with various purposes in mind. In this chapter, we will discuss the advantages and disadvantages of using SNPs for human identification...... of SNPs. This will allow acquisition of more information from the sample materials and open up for new possibilities as well as new challenges....

  11. Clustered DNA lesions containing 5-formyluracil and AP site: repair via the BER system.

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    Ekaterina A Belousova

    Full Text Available Lesions in the DNA arise under ionizing irradiation conditions or various chemical oxidants as a single damage or as part of a multiply damaged site within 1-2 helical turns (clustered lesion. Here, we explored the repair opportunity of the apurinic/apyrimidinic site (AP site composed of the clustered lesion with 5-formyluracil (5-foU by the base excision repair (BER proteins. We found, that if the AP site is shifted relative to the 5-foU of the opposite strand, it could be repaired primarily via the short-patch BER pathway. In this case, the cleavage efficiency of the AP site-containing DNA strand catalyzed by human apurinic/apyrimidinic endonuclease 1 (hAPE1 decreased under AP site excursion to the 3'-side relative to the lesion in the other DNA strand. DNA synthesis catalyzed by DNA polymerase lambda was more accurate in comparison to the one catalyzed by DNA polymerase beta. If the AP site was located exactly opposite 5-foU it was expected to switch the repair to the long-patch BER pathway. In this situation, human processivity factor hPCNA stimulates the process.

  12. The regulated secretory pathway and human disease: insights from gene variants and single nucleotide polymorphisms

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    Stephen eSalton

    2013-08-01

    Full Text Available The regulated secretory pathway provides critical control of peptide, growth factor, and hormone release from neuroendocrine and endocrine cells, and neurons, maintaining physiological homeostasis. Propeptides and prohormones are packaged into dense core granules (DCGs, where they frequently undergo tissue-specific processing as the DCG matures. Proteins of the granin family are DCG components, and although their function is not fully understood, data suggest they are involved in DCG formation and regulated protein/peptide secretion, in addition to their role as precursors of bioactive peptides. Association of gene variation, including single nucleotide polymorphisms (SNPs, with neuropsychiatric, endocrine and metabolic diseases, has implicated specific secreted proteins and peptides in disease pathogenesis. For example, a SNP at position 196 (G/A of the human brain-derived neurotrophic factor (BDNF gene dysregulates protein processing and secretion and leads to cognitive impairment. This suggests more generally that variants identified in genes encoding secreted growth factors, peptides, hormones, and proteins involved in DCG biogenesis, protein processing, and the secretory apparatus, could provide insight into the process of regulated secretion as well as disorders that result when it is impaired.

  13. An Engineered Kinetic Amplification Mechanism for Single Nucleotide Variant Discrimination by DNA Hybridization Probes.

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    Chen, Sherry Xi; Seelig, Georg

    2016-04-20

    Even a single-nucleotide difference between the sequences of two otherwise identical biological nucleic acids can have dramatic functional consequences. Here, we use model-guided reaction pathway engineering to quantitatively improve the performance of selective hybridization probes in recognizing single nucleotide variants (SNVs). Specifically, we build a detection system that combines discrimination by competition with DNA strand displacement-based catalytic amplification. We show, both mathematically and experimentally, that the single nucleotide selectivity of such a system in binding to single-stranded DNA and RNA is quadratically better than discrimination due to competitive hybridization alone. As an additional benefit the integrated circuit inherits the property of amplification and provides at least 10-fold better sensitivity than standard hybridization probes. Moreover, we demonstrate how the detection mechanism can be tuned such that the detection reaction is agnostic to the position of the SNV within the target sequence. in contrast, prior strand displacement-based probes designed for kinetic discrimination are highly sensitive to position effects. We apply our system to reliably discriminate between different members of the let-7 microRNA family that differ in only a single base position. Our results demonstrate the power of systematic reaction network design to quantitatively improve biotechnology.

  14. Single nucleotide polymorphisms as susceptibility, prognostic, and therapeutic markers of nonsmall cell lung cancer

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    Zienolddiny S

    2011-12-01

    Full Text Available Shanbeh Zienolddiny, Vidar SkaugSection for Toxicology and Biological Work Environment, National Institute of Occupational Health, Oslo, NorwayAbstract: Lung cancer is a major public health problem throughout the world. Among the most frequent cancer types (prostate, breast, colorectal, stomach, lung, lung cancer is the leading cause of cancer-related deaths worldwide. Among the two major subtypes of small cell lung cancer and nonsmall cell lung cancer (NSCLC, 85% of tumors belong to the NSCLC histological types. Small cell lung cancer is associated with the shortest survival time. Although tobacco smoking has been recognized as the major risk factor for lung cancer, there is a great interindividual and interethnic difference in risk of developing lung cancer given exposure to similar environmental and lifestyle factors. This may indicate that in addition to chemical and environmental factors, genetic variations in the genome may contribute to risk modification. A common type of genetic variation in the genome, known as single nucleotide polymorphism, has been found to be associated with susceptibility to lung cancer. Interestingly, many of these polymorphisms are found in the genes that regulate major pathways of carcinogen metabolism (cytochrome P450 genes, detoxification (glutathione S-transferases, adduct removal (DNA repair genes, cell growth/apoptosis (TP53/MDM2, the immune system (cytokines/chemokines, and membrane receptors (nicotinic acetylcholine and dopaminergic receptors. Some of these polymorphisms have been shown to alter the level of mRNA, and protein structure and function. In addition to being susceptibility markers, several of these polymorphisms are emerging to be important for response to chemotherapy/radiotherapy and survival of patients. Therefore, it is hypothesized that single nucleotide polymorphisms will be valuable genetic markers in individual-based prognosis and therapy in future. Here we will review some of the most

  15. In-silico single nucleotide polymorphisms (SNP) mining of Sorghum ...

    African Journals Online (AJOL)

    Single nucleotide polymorphisms (SNPs) may be considered the ultimate genetic markers as they represent the finest resolution of a DNA sequence (a single nucleotide), and are generally abundant in populations with a low mutation rate. SNPs are important tools in studying complex genetic traits and genome evolution.

  16. Understanding specificity in metabolic pathways-Structural biology of human nucleotide metabolism

    International Nuclear Information System (INIS)

    Welin, Martin; Nordlund, Paer

    2010-01-01

    Interactions are the foundation of life at the molecular level. In the plethora of activities in the cell, the evolution of enzyme specificity requires the balancing of appropriate substrate affinity with a negative selection, in order to minimize interactions with other potential substrates in the cell. To understand the structural basis for enzyme specificity, the comparison of structural and biochemical data between enzymes within pathways using similar substrates and effectors is valuable. Nucleotide metabolism is one of the largest metabolic pathways in the human cell and is of outstanding therapeutic importance since it activates and catabolises nucleoside based anti-proliferative drugs and serves as a direct target for anti-proliferative drugs. In recent years the structural coverage of the enzymes involved in human nucleotide metabolism has been dramatically improved and is approaching completion. An important factor has been the contribution from the Structural Genomics Consortium (SGC) at Karolinska Institutet, which recently has solved 33 novel structures of enzymes and enzyme domains in human nucleotide metabolism pathways and homologs thereof. In this review we will discuss some of the principles for substrate specificity of enzymes in human nucleotide metabolism illustrated by a selected set of enzyme families where a detailed understanding of the structural determinants for specificity is now emerging.

  17. An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

    International Nuclear Information System (INIS)

    Wang Zhan-Feng; Liu Yu-Ru; Wang Peng-Ye; Xie Ping

    2017-01-01

    Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate (NTP) selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre- and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre- and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson–Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA–RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTP. (paper)

  18. Quantum Point Contact Single-Nucleotide Conductance for DNA and RNA Sequence Identification.

    Science.gov (United States)

    Afsari, Sepideh; Korshoj, Lee E; Abel, Gary R; Khan, Sajida; Chatterjee, Anushree; Nagpal, Prashant

    2017-11-28

    Several nanoscale electronic methods have been proposed for high-throughput single-molecule nucleic acid sequence identification. While many studies display a large ensemble of measurements as "electronic fingerprints" with some promise for distinguishing the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine, and uracil), important metrics such as accuracy and confidence of base calling fall well below the current genomic methods. Issues such as unreliable metal-molecule junction formation, variation of nucleotide conformations, insufficient differences between the molecular orbitals responsible for single-nucleotide conduction, and lack of rigorous base calling algorithms lead to overlapping nanoelectronic measurements and poor nucleotide discrimination, especially at low coverage on single molecules. Here, we demonstrate a technique for reproducible conductance measurements on conformation-constrained single nucleotides and an advanced algorithmic approach for distinguishing the nucleobases. Our quantum point contact single-nucleotide conductance sequencing (QPICS) method uses combed and electrostatically bound single DNA and RNA nucleotides on a self-assembled monolayer of cysteamine molecules. We demonstrate that by varying the applied bias and pH conditions, molecular conductance can be switched ON and OFF, leading to reversible nucleotide perturbation for electronic recognition (NPER). We utilize NPER as a method to achieve >99.7% accuracy for DNA and RNA base calling at low molecular coverage (∼12×) using unbiased single measurements on DNA/RNA nucleotides, which represents a significant advance compared to existing sequencing methods. These results demonstrate the potential for utilizing simple surface modifications and existing biochemical moieties in individual nucleobases for a reliable, direct, single-molecule, nanoelectronic DNA and RNA nucleotide identification method for sequencing.

  19. The immediate nucleotide precursor, guanosine triphosphate, in the riboflavin biosynthetic pathway

    International Nuclear Information System (INIS)

    Mitsuda, Hisateru; Nakajima, Kenji; Nadamoto, Tomonori

    1977-01-01

    In the present paper, the nucleotide precursor of riboflavin was investigated by experiments with labeled purines using non-growing cells of Eremothecium ashbyii. The added purines, at 10 -4 M, were effectively incorporated into riboflavin at an early stage of riboflavin biosynthesis under the experimental conditions. In particular, both labeled xanthine and labeled guanine were specifically transported to guanosine nucleotides, GMP, GDP, GDP-Mannose and GTP, in the course of the riboflavin biosynthesis. A comparison of specific activities of labeled guanosine nucleotides and labeled riboflavin indicated that the nucleotide precursor of riboflavin is guanosine triphosphate. From the results obtained, a biosynthetic pathway of riboflavin is proposed. (auth.)

  20. Both base excision repair and nucleotide excision repair in humans are influenced by nutritional factors.

    Science.gov (United States)

    Brevik, Asgeir; Karlsen, Anette; Azqueta, Amaya; Tirado, Anna Estaban; Blomhoff, Rune; Collins, Andrew

    2011-01-01

    Lack of reliable assays for DNA repair has largely prevented measurements of DNA repair from being included in human biomonitoring studies. Using newly developed modifications of the comet assay we tested whether a fruit- and antioxidant-rich plant-based intervention could affect base excision repair (BER) and nucleotide excision repair (NER) in a group of 102 male volunteers. BER and NER repair capacities were measured in lymphocytes before and after a dietary intervention lasting 8 weeks. The study had one control group, one group consuming three kiwifruits per day and one group consuming a variety of antioxidant-rich fruits and plant products in addition to their normal diet. DNA strand breaks were reduced following consumption of both kiwifruits (13%, p = 0.05) and antioxidant-rich plant products (20%, p = 0.02). Increased BER (55%, p = 0.01) and reduced NER (-39%, p plant products. Reduced NER was also observed in the kiwifruit group (-38%, p = 0.05), but BER was not affected in this group. Here we have demonstrated that DNA repair is affected by diet and that modified versions of the comet assay can be used to assess activity of different DNA repair pathways in human biomonitoring studies. Copyright © 2010 John Wiley & Sons, Ltd.

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

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

    2013-11-15

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

  2. Direct detection of single-nucleotide polymorphisms in bacterial DNA by SNPtrap

    DEFF Research Database (Denmark)

    Grønlund, Hugo Ahlm; Moen, Birgitte; Hoorfar, Jeffrey

    2011-01-01

    A major challenge with single-nucleotide polymorphism (SNP) fingerprinting of bacteria and higher organisms is the combination of genome-wide screenings with the potential of multiplexing and accurate SNP detection. Single-nucleotide extension by the minisequencing principle represents a technolo...

  3. MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways

    Science.gov (United States)

    Koumakis, Lefteris; Kartsaki, Evgenia; Chatzimina, Maria; Zervakis, Michalis; Vassou, Despoina; Marias, Kostas; Moustakis, Vassilis; Potamias, George

    2016-01-01

    Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  5. Evaluation of the XRCC1 gene as a phenotypic modifier in BRCA1/2 mutation carriers. Results from the consortium of investigators of modifiers of BRCA1/BRCA2

    NARCIS (Netherlands)

    Osorio, A.; Milne, R. L.; Alonso, R.; Pita, G.; Peterlongo, P.; Teulé, A.; Nathanson, K. L.; Domchek, S. M.; Rebbeck, T.; Lasa, A.; Konstantopoulou, I.; Hogervorst, F. B.; Verhoef, S.; van Dooren, M. F.; Jager, A.; Ausems, M. G. E. M.; Aalfs, C. M.; van Asperen, C. J.; Vreeswijk, M.; Waisfisz, Q.; van Roozendaal, C. E.; Ligtenberg, M. J.; Easton, D. F.; Peock, S.; Cook, M.; Oliver, C. T.; Frost, D.; Curzon, B.; Evans, D. G.; Lalloo, F.; Eeles, R.; Izatt, L.; Davidson, R.; Adlard, J.; Eccles, D.; Ong, K.-r; Douglas, F.; Downing, S.; Brewer, C.; Walker, L.; Nevanlinna, H.; Aittomäki, K.; Couch, F. J.; Fredericksen, Z.; Lindor, N. M.; Godwin, A.; Isaacs, C.; Caligo, M. A.; Loman, N.; Jernström, H.; Barbany-Bustinza, G.; Liljegren, A.; Ehrencrona, H.; Stenmark-Askmalm, M.; Feliubadaló, L.; Manoukian, S.; Peissel, B.; Zaffaroni, D.; Bonanni, B.; Fortuzzi, S.; Johannsson, O. T.; Chenevix-Trench, G.; Chen, X.-C.; Beesley, J.; Spurdle, A. B.; Sinilnikova, O. M.; Healey, S.; McGuffog, L.; Antoniou, A. C.; Brunet, J.; Radice, P.; Benítez, J.; Hogervorst, F. B. L.; Verheus, M.; van 't Veer, L. J.; van Leeuwen, F. E.; Rookus, M. A.; Collée, M.; van den Ouweland, A. M. W.; Hooning, M. J.; Tilanus-Linthorst, M. M. A.; Seynaeve, C.; Wijnen, J. T.; Vreeswijk, M. P.; Tollenaar, R. A.; Devilee, P.; Hoogerbrugge, N.; Ausems, M. G.; van der Luijt, R. B.; van Os, T. A.; Gille, J. J. P.; Meijers-Heijboer, H. E. J.; Gomez-Garcia, E. B.; Blok, Marinus J.; Caanen, B.; Oosterwijk, J. C.; van der Hout, A. H.; Mourits, M. J.; Vasen, H. F.; Peock, Susan; Cook, Margaret; Oliver, Clare; Frost, Debra; Miedzybrodzka, Zosia; Gregory, Helen; Morrison, Patrick; Jeffers, Lisa; Cole, Trevor; McKeown, Carole; Ong, Kai-Ren; Hoffman, Jonathan; Donaldson, Alan; Paterson, Joan; Downing, Sarah; Taylor, Amy; Murray, Alexandra; Rogers, Mark T.; McCann, Emma; Kennedy, M. John; Barton, David; East, South; Porteous, Mary; Drummond, Sarah; Brewer, Carole; Kivuva, Emma; Searle, Anne; Goodman, Selina; Hill, Kathryn; Davidson, Rosemarie; Bradshaw, Nicola; Snadden, Lesley; Longmuir, Mark; Watt, Catherine; Gibson, Sarah; Izatt, Louise; Jacobs, Chris; Langman, Caroline; Whaite, Anna; Dorkins, Huw; Barwell, Julian; Adlard, Julian; Chu, Carol; Miller, Julie; Ellis, Ian; Evans, D. Gareth; Lalloo, Fiona; Taylor, Jane; Side, Lucy; Male, Alison; Berlin, Cheryl; Eason, Jacqueline; Collier, Rebecca; Douglas, Fiona; Claber, Oonagh; Walker, Lisa; McLeod, Diane; Halliday, Dorothy; Durell, Sarah; Stayner, Barbara; Eeles, Ros; Shanley, Susan; Rahman, Nazneen; Houlston, Richard; Bancroft, Elizabeth; D'Mello, Lucia; Page, Elizabeth; Ardern-Jones, Audrey; Kohut, Kelly; Wiggins, Jennifer; Castro, Elena; Mitra, Anitra; Robertson, Lisa; Cook, Jackie; Quarrell, Oliver; Bardsley, Cathryn; Hodgson, Shirley; Goff, Sheila; Brice, Glen; Winchester, Lizzie; Eddy, Charlotte; Tripathi, Vishakha; Attard, Virginia; Eccles, Diana; Lucassen, Anneke; Crawford, Gillian; McBride, Donna; Smalley, Sarah; Godwin, A. K.; Karlsson, Per; Nordling, Margareta; Bergman, Annika; Einbeigi, Zakaria; Stenmark- Askmalm, Marie; Liedgren, Sigrun; Borg, Ake; Loman, Niklas; Olsson, Håkan; Kristoffersson, Ulf; Jernström, Helena; Harbst, Katja; Henriksson, Karin; Lindblom, Annika; Arver, Brita; Wachenfeldt, Anna von; Liljegren, Annelie; Barbany-Bustinza, Gisela; Rantala, Johanna; Melin, Beatrice; Grönberg, Henrik; Stattin, Eva-Lena; Emanuelsson, Monica; Ehrencrona, Hans; Rosenquist Brandell, Richard; Dahl, Niklas

    2011-01-01

    Single-nucleotide polymorphisms (SNPs) in genes involved in DNA repair are good candidates to be tested as phenotypic modifiers for carriers of mutations in the high-risk susceptibility genes BRCA1 and BRCA2. The base excision repair (BER) pathway could be particularly interesting given the relation

  6. Investigation of single nucleotide polymorphisms and biological pathways associated with response to TNFα inhibitors in patients with rheumatoid arthritis

    DEFF Research Database (Denmark)

    Krintel, Sophine B; Palermo, Giuseppe; Johansen, Julia S

    2012-01-01

    Recently, two genome-wide association studies identified single nucleotide polymorphisms (SNPs) significantly associated with the treatment response to tumor necrosis factor α (TNFα) inhibitors in patients with rheumatoid arthritis (RA). We aimed to replicate these results and identify SNPs and t...

  7. Efficiency and Fidelity of Human DNA Polymerases λ and β during Gap-Filling DNA Synthesis

    Science.gov (United States)

    Brown, Jessica A.; Pack, Lindsey R.; Sanman, Laura E.; Suo, Zucai

    2010-01-01

    The base excision repair (BER) pathway coordinates the replacement of 1 to 10 nucleotides at sites of single-base lesions. This process generates DNA substrates with various gap sizes which can alter the catalytic efficiency and fidelity of a DNA polymerase during gap-filling DNA synthesis. Here, we quantitatively determined the substrate specificity and base substitution fidelity of human DNA polymerase λ (Pol λ), an enzyme proposed to support the known BER DNA polymerase β (Pol β), as it filled 1- to 10-nucleotide gaps at 1-nucleotide intervals. Pol λ incorporated a correct nucleotide with relatively high efficiency until the gap size exceeded 9 nucleotides. Unlike Pol λ, Pol β did not have an absolute threshold on gap size as the catalytic efficiency for a correct dNTP gradually decreased as the gap size increased from 2 to 10 nucleotides and then recovered for non-gapped DNA. Surprisingly, an increase in gap size resulted in lower polymerase fidelity for Pol λ, and this downregulation of fidelity was controlled by its non-enzymatic N-terminal domains. Overall, Pol λ was up to 160-fold more error-prone than Pol β, thereby suggesting Pol λ would be more mutagenic during long gap-filling DNA synthesis. In addition, dCTP was the preferred misincorporation for Pol λ and its N-terminal domain truncation mutants. This nucleotide preference was shown to be dependent upon the identity of the adjacent 5′-template base. Our results suggested that both Pol λ and Pol β would catalyze nucleotide incorporation with the highest combination of efficiency and accuracy when the DNA substrate contains a single-nucleotide gap. Thus, Pol λ, like Pol β, is better suited to catalyze gap-filling DNA synthesis during short-patch BER in vivo, although, Pol λ may play a role in long-patch BER. PMID:20961817

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

    NARCIS (Netherlands)

    Osorio, A.; Milne, R.L.; Kuchenbaecker, K.; Vaclova, T.; Pita, G.; Alonso, R.; Peterlongo, P.; Blanco, I.; Hoya, M. de la; Duran, M.; Diez, O.; Ramon, Y.C.T.; Konstantopoulou, I.; Martinez-Bouzas, C.; Conejero, R. Andres; Soucy, P.; McGuffog, L.; Barrowdale, D.; Lee, A.; Swe, B.; Arver, B.; Rantala, J.; Loman, N.; Ehrencrona, H.; Olopade, O.I.; Beattie, M.S.; Domchek, S.M.; Nathanson, K.; Rebbeck, T.R.; Arun, B.K.; Karlan, B.Y.; Walsh, C.; Lester, J.; John, E.M.; Whittemore, A.S.; Daly, M.B.; Southey, M.; Hopper, J.; Terry, M.B.; Buys, S.S.; Janavicius, R.; Dorfling, C.M.; Rensburg, E.J. van; Steele, L.; Neuhausen, S.L.; Ding, Y.C.; Hansen, T.V.; Jonson, L.; Ejlertsen, B.; Gerdes, A.M.; Infante, M.; Herraez, B.; Moreno, L.T.; Weitzel, J.N.; Herzog, J.; Weeman, K.; Manoukian, S.; Peissel, B.; Zaffaroni, D.; Scuvera, G.; Bonanni, B.; Mariette, F.; Volorio, S.; Viel, A.; Varesco, L.; Papi, L.; Ottini, L.; Tibiletti, M.G.; Radice, P.; Yannoukakos, D.; Garber, J.; Ellis, S.; Frost, D.; Platte, R.; Fineberg, E.; Evans, G.; Lalloo, F.; Izatt, L.; Eeles, R.; Adlard, J.; Davidson, R.; Cole, T.; Eccles, D.; Cook, J; Hodgson, S.; Brewer, C.; Tischkowitz, M.; Douglas, F.; Porteous, M.; Side, L.; Walker, L.; Morrison, P.; Donaldson, A.; Kennedy, J.; Foo, C.; Godwin, A.K.; Schmutzler, R.K.; Wappenschmidt, B.; Rhiem, K.; Engel, C.; Hoogerbrugge-van der Linden, N.; et al.,

    2014-01-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  10. A single nucleotide polymorphism (SNP) assay for population ...

    African Journals Online (AJOL)

    A single nucleotide polymorphism (SNP) assay for population stratification test ... phenotypes and unlinked candidate loci in case-control and cohort studies of ... Key words: Chinese, Japanese, population stratification, ancestry informative ...

  11. Regulation of Burkholderia cenocepacia biofilm formation by RpoN and the c-di-GMP effector BerB

    DEFF Research Database (Denmark)

    Fazli, Mustafa; Rybtke, Morten Levin; Steiner, Elisabeth

    2017-01-01

    Knowledge about the molecular mechanisms that are involved in the regulation of biofilm formation is essential for the development of biofilm-control measures. It is well established that the nucleotide second messenger cyclic diguanosine monophosphate (c-di-GMP) is a positive regulator of biofilm...... formation in many bacteria, but more knowledge about c-di-GMP effectors is needed. We provide evidence that c-di-GMP, the alternative sigma factor RpoN (σ54), and the enhancer-binding protein BerB play a role in biofilm formation of Burkholderia cenocepacia by regulating the production of a biofilm......-stabilizing exopolysaccharide. Our findings suggest that BerB binds c-di-GMP, and activates RpoN-dependent transcription of the berA gene coding for a c-di-GMP-responsive transcriptional regulator. An increased level of the BerA protein in turn induces the production of biofilm-stabilizing exopolysaccharide in response to high...

  12. Correlations between clinical normal tissue radiosensitivity and single nucleotide polymorphisms in ATM, XRCC1, XRCC3, APEX, SOD2, and TGF-B1

    DEFF Research Database (Denmark)

    Alsner, Jan; Andreassen, Christian Nicolaj; Overgaard, Marie

    in biological pathways suspected to underlie phenotypes of interest. These variants can be either common alterations like single nucleotide polymorphisms, SNPs, or rare variants in potential susceptibility loci like ATM. In parallel, we are using microarray analysis on normal fibroblasts isolated from patients...

  13. DNA polymerases beta and lambda mediate overlapping and independent roles in base excision repair in mouse embryonic fibroblasts.

    Directory of Open Access Journals (Sweden)

    Elena K Braithwaite

    2010-08-01

    Full Text Available Base excision repair (BER is a DNA repair pathway designed to correct small base lesions in genomic DNA. While DNA polymerase beta (pol beta is known to be the main polymerase in the BER pathway, various studies have implicated other DNA polymerases in back-up roles. One such polymerase, DNA polymerase lambda (pol lambda, was shown to be important in BER of oxidative DNA damage. To further explore roles of the X-family DNA polymerases lambda and beta in BER, we prepared a mouse embryonic fibroblast cell line with deletions in the genes for both pol beta and pol lambda. Neutral red viability assays demonstrated that pol lambda and pol beta double null cells were hypersensitive to alkylating and oxidizing DNA damaging agents. In vitro BER assays revealed a modest contribution of pol lambda to single-nucleotide BER of base lesions. Additionally, using co-immunoprecipitation experiments with purified enzymes and whole cell extracts, we found that both pol lambda and pol beta interact with the upstream DNA glycosylases for repair of alkylated and oxidized DNA bases. Such interactions could be important in coordinating roles of these polymerases during BER.

  14. Pervasive within-Mitochondrion Single-Nucleotide Variant Heteroplasmy as Revealed by Single-Mitochondrion Sequencing

    Directory of Open Access Journals (Sweden)

    Jacqueline Morris

    2017-12-01

    Full Text Available Summary: A number of mitochondrial diseases arise from single-nucleotide variant (SNV accumulation in multiple mitochondria. Here, we present a method for identification of variants present at the single-mitochondrion level in individual mouse and human neuronal cells, allowing for extremely high-resolution study of mitochondrial mutation dynamics. We identified extensive heteroplasmy between individual mitochondrion, along with three high-confidence variants in mouse and one in human that were present in multiple mitochondria across cells. The pattern of variation revealed by single-mitochondrion data shows surprisingly pervasive levels of heteroplasmy in inbred mice. Distribution of SNV loci suggests inheritance of variants across generations, resulting in Poisson jackpot lines with large SNV load. Comparison of human and mouse variants suggests that the two species might employ distinct modes of somatic segregation. Single-mitochondrion resolution revealed mitochondria mutational dynamics that we hypothesize to affect risk probabilities for mutations reaching disease thresholds. : Morris et al. use independent sequencing of multiple individual mitochondria from mouse and human brain cells to show high pervasiveness of mutations. The mutations are heteroplasmic within single mitochondria and within and between cells. These findings suggest mechanisms by which mutations accumulate over time, resulting in mitochondrial dysfunction and disease. Keywords: single mitochondrion, single cell, human neuron, mouse neuron, single-nucleotide variation

  15. Single Nucleotide Polymorphism Detection Using Au-Decorated Single-Walled Carbon Nanotube Field Effect Transistors

    Directory of Open Access Journals (Sweden)

    Keum-Ju Lee

    2011-01-01

    Full Text Available We demonstrate that Au-cluster-decorated single-walled carbon nanotubes (SWNTs may be used to discriminate single nucleotide polymorphism (SNP. Nanoscale Au clusters were formed on the side walls of carbon nanotubes in a transistor geometry using electrochemical deposition. The effect of Au cluster decoration appeared as hole doping when electrical transport characteristics were examined. Thiolated single-stranded probe peptide nucleic acid (PNA was successfully immobilized on Au clusters decorating single-walled carbon nanotube field-effect transistors (SWNT-FETs, resulting in a conductance decrease that could be explained by a decrease in Au work function upon adsorption of thiolated PNA. Although a target single-stranded DNA (ssDNA with a single mismatch did not cause any change in electrical conductance, a clear decrease in conductance was observed with matched ssDNA, thereby showing the possibility of SNP (single nucleotide polymorphism detection using Au-cluster-decorated SWNT-FETs. However, a power to discriminate SNP target is lost in high ionic environment. We can conclude that observed SNP discrimination in low ionic environment is due to the hampered binding of SNP target on nanoscale surfaces in low ionic conditions.

  16. The BER necessities: the repair of DNA damage in human-adapted bacterial pathogens.

    Science.gov (United States)

    van der Veen, Stijn; Tang, Christoph M

    2015-02-01

    During colonization and disease, bacterial pathogens must survive the onslaught of the host immune system. A key component of the innate immune response is the generation of reactive oxygen and nitrogen species by phagocytic cells, which target and disrupt pathogen molecules, particularly DNA, and the base excision repair (BER) pathway is the most important mechanism for the repair of such oxidative DNA damage. In this Review, we discuss how the human-specific pathogens Mycobacterium tuberculosis, Helicobacter pylori and Neisseria meningitidis have evolved specialized mechanisms of DNA repair, particularly their BER pathways, compared with model organisms such as Escherichia coli. This specialization in DNA repair is likely to reflect the distinct niches occupied by these important human pathogens in the host.

  17. Development of a single nucleotide polymorphism (SNP) marker for ...

    African Journals Online (AJOL)

    The nature of the single nucleotide polymorphism (SNP) marker was validated by DNA sequencing of the parental PCR products. Using high resolution melt (HRM) profiles and normalised difference plots, we successfully differentiated the homozygous dominant (wild type), homozygous recessive (LPA) and heterozygous ...

  18. Minimum BER Receiver Filters with Block Memory for Uplink DS-CDMA Systems

    Directory of Open Access Journals (Sweden)

    Debbah Mérouane

    2008-01-01

    Full Text Available Abstract The problem of synchronous multiuser receiver design in the case of direct-sequence single-antenna code division multiple access (DS-CDMA uplink networks is studied over frequency selective fading channels. An exact expression for the bit error rate (BER is derived in the case of BPSK signaling. Moreover, an algorithm is proposed for finding the finite impulse response (FIR receiver filters with block memory such that the exact BER of the active users is minimized. Several properties of the minimum BER FIR filters with block memory are identified. The algorithm performance is found for scenarios with different channel qualities, spreading code lengths, receiver block memory size, near-far effects, and channel mismatch. For the BPSK constellation, the proposed FIR receiver structure with block memory has significant better BER with respect to and near-far resistance than the corresponding minimum mean square error (MMSE filters with block memory.

  19. Minimum BER Receiver Filters with Block Memory for Uplink DS-CDMA Systems

    Directory of Open Access Journals (Sweden)

    Mérouane Debbah

    2008-05-01

    Full Text Available The problem of synchronous multiuser receiver design in the case of direct-sequence single-antenna code division multiple access (DS-CDMA uplink networks is studied over frequency selective fading channels. An exact expression for the bit error rate (BER is derived in the case of BPSK signaling. Moreover, an algorithm is proposed for finding the finite impulse response (FIR receiver filters with block memory such that the exact BER of the active users is minimized. Several properties of the minimum BER FIR filters with block memory are identified. The algorithm performance is found for scenarios with different channel qualities, spreading code lengths, receiver block memory size, near-far effects, and channel mismatch. For the BPSK constellation, the proposed FIR receiver structure with block memory has significant better BER with respect to Eb/N0 and near-far resistance than the corresponding minimum mean square error (MMSE filters with block memory.

  20. Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time.

    Science.gov (United States)

    Kong, Muwen; Beckwitt, Emily C; Springall, Luke; Kad, Neil M; Van Houten, Bennett

    2017-01-01

    Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways. In this chapter, we demonstrate the utility of the platform by applying these techniques in the studies of proteins participating in nucleotide excision repair. © 2017 Elsevier Inc. All rights reserved.

  1. Adiponectin Single Nucleotide Polymorphism (+276G/T) and Its ...

    African Journals Online (AJOL)

    The present study was investigating the association between the single nucleotide polymorphism +276 G/T of the adiponectin gene with serum adiponectin level in patients with coronary artery disease (CAD). In this study 100 healthy controls and 100 Egyptian patients with coronary artery disease of both genders ...

  2. Infectious mononucleosis-linked HLA class I single nucleotide polymorphism is associated with multiple sclerosis.

    Science.gov (United States)

    Jafari, Naghmeh; Broer, Linda; Hoppenbrouwers, Ilse A; van Duijn, Cornelia M; Hintzen, Rogier Q

    2010-11-01

    Multiple sclerosis is a presumed autoimmune disease associated with genetic and environmental risk factors such as infectious mononucleosis. Recent research has shown infectious mononucleosis to be associated with a specific HLA class I polymorphism. Our aim was to test if the infectious mononucleosis-linked HLA class I single nucleotide polymorphism (rs6457110) is also associated with multiple sclerosis. Genotyping of the HLA-A single nucleotide polymorphism rs6457110 using TaqMan was performed in 591 multiple sclerosis cases and 600 controls. The association of multiple sclerosis with the HLA-A single nucleotide polymorphism was tested using logistic regression adjusted for age, sex and HLA-DRB1*1501. HLA-A minor allele (A) is associated with multiple sclerosis (OR = 0.68; p = 4.08 × 10( -5)). After stratification for HLA-DRB1*1501 risk allele (T) carrier we showed a significant OR of 0.70 (p = 0.003) for HLA-A. HLA class I single nucleotide polymorphism rs6457110 is associated with infectious mononucleosis and multiple sclerosis, independent of the major class II allele, supporting the hypothesis that shared genetics may contribute to the association between infectious mononucleosis and multiple sclerosis.

  3. Single-Nucleotide Variations in Cardiac Arrhythmias: Prospects for Genomics and Proteomics Based Biomarker Discovery and Diagnostics

    Directory of Open Access Journals (Sweden)

    Ayman Abunimer

    2014-03-01

    Full Text Available Cardiovascular diseases are a large contributor to causes of early death in developed countries. Some of these conditions, such as sudden cardiac death and atrial fibrillation, stem from arrhythmias—a spectrum of conditions with abnormal electrical activity in the heart. Genome-wide association studies can identify single nucleotide variations (SNVs that may predispose individuals to developing acquired forms of arrhythmias. Through manual curation of published genome-wide association studies, we have collected a comprehensive list of 75 SNVs associated with cardiac arrhythmias. Ten of the SNVs result in amino acid changes and can be used in proteomic-based detection methods. In an effort to identify additional non-synonymous mutations that affect the proteome, we analyzed the post-translational modification S-nitrosylation, which is known to affect cardiac arrhythmias. We identified loss of seven known S-nitrosylation sites due to non-synonymous single nucleotide variations (nsSNVs. For predicted nitrosylation sites we found 1429 proteins where the sites are modified due to nsSNV. Analysis of the predicted S-nitrosylation dataset for over- or under-representation (compared to the complete human proteome of pathways and functional elements shows significant statistical over-representation of the blood coagulation pathway. Gene Ontology (GO analysis displays statistically over-represented terms related to muscle contraction, receptor activity, motor activity, cystoskeleton components, and microtubule activity. Through the genomic and proteomic context of SNVs and S-nitrosylation sites presented in this study, researchers can look for variation that can predispose individuals to cardiac arrhythmias. Such attempts to elucidate mechanisms of arrhythmia thereby add yet another useful parameter in predicting susceptibility for cardiac diseases.

  4. Electrical detection and quantification of single and mixed DNA nucleotides in suspension

    Science.gov (United States)

    Ahmad, Mahmoud Al; Panicker, Neena G.; Rizvi, Tahir A.; Mustafa, Farah

    2016-09-01

    High speed sequential identification of the building blocks of DNA, (deoxyribonucleotides or nucleotides for short) without labeling or processing in long reads of DNA is the need of the hour. This can be accomplished through exploiting their unique electrical properties. In this study, the four different types of nucleotides that constitute a DNA molecule were suspended in a buffer followed by performing several types of electrical measurements. These electrical parameters were then used to quantify the suspended DNA nucleotides. Thus, we present a purely electrical counting scheme based on the semiconductor theory that allows one to determine the number of nucleotides in a solution by measuring their capacitance-voltage dependency. The nucleotide count was observed to be similar to the multiplication of the corresponding dopant concentration and debye volume after de-embedding the buffer contribution. The presented approach allows for a fast and label-free quantification of single and mixed nucleotides in a solution.

  5. Nucleotide Metabolism

    DEFF Research Database (Denmark)

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

    2011-01-01

    Metabolic pathways are connected through their utilization of nucleotides as supplier of energy, allosteric effectors, and their role in activation of intermediates. Therefore, any attempt to exploit a given living organism in a biotechnological process will have an impact on nucleotide metabolis...

  6. Predicting metabolic pathways by sub-network extraction.

    Science.gov (United States)

    Faust, Karoline; van Helden, Jacques

    2012-01-01

    Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more enzyme-coding genes, graph analysis methods can be applied to extract a metabolic pathway that interconnects them. We describe here the way to use the Pathway extraction tool available on the NeAT Web server ( http://rsat.ulb.ac.be/neat/ ) to piece together the metabolic pathway from a group of associated, enzyme-coding genes. The tool identifies the reactions that can be catalyzed by the products of the query genes (seed reactions), and applies sub-graph extraction algorithms to extract from a metabolic network a sub-network that connects the seed reactions. This sub-network represents the predicted metabolic pathway. We describe here the pathway prediction process in a step-by-step way, give hints about the main parametric choices, and illustrate how this tool can be used to extract metabolic pathways from bacterial genomes, on the basis of two study cases: the isoleucine-valine operon in Escherichia coli and a predicted operon in Cupriavidus (Ralstonia) metallidurans.

  7. Purification, crystallization and initial crystallographic characterization of brazil-nut allergen Ber e 2

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Feng; Jin, Tengchuan; Howard, Andrew; Zhang, Yu-Zhu, E-mail: zhangy@iit.edu [Department of Biology, Illinois Institute of Technology, Chicago, IL 60616 (United States)

    2007-11-01

    The crystallization of the brazil nut allergen Ber e 2 is reported. Peanut and tree-nut allergies have attracted considerable attention because of their frequency and their lifelong persistence. Brazil-nut (Bertholletia excelsa) allergies have been well documented and the 11S legumin-like seed storage protein Ber e 2 (excelsin) is one of the two known brazil-nut allergens. In this study, Ber e 2 was extracted from brazil-nut kernels and purified to high purity by crystalline precipitation and gel-filtration chromatography. Well diffracting single crystals were obtained using the hanging-drop vapour-diffusion method. A molecular-replacement structural solution has been obtained. Refinement of the structure is currently under way.

  8. Four new single nucleotide polymorphisms (SNPs) of toll-like ...

    African Journals Online (AJOL)

    In order to reveal the single nucleotide polymorphisms (SNPs), genotypes and allelic frequencies of each mutation site of TLR7 gene in Chinese native duck breeds, SNPs of duck TLR7 gene were detected by DNA sequencing. The genotypes of 465 native ducks from eight key protected duck breeds were determined by ...

  9. A history of the DNA repair and mutagenesis field: The discovery of base excision repair.

    Science.gov (United States)

    Friedberg, Errol C

    2016-01-01

    This article reviews the early history of the discovery of an DNA repair pathway designated as base excision repair (BER), since in contrast to the enzyme-catalyzed removal of damaged bases from DNA as nucleotides [called nucleotide excision repair (NER)], BER involves the removal of damaged or inappropriate bases, such as the presence of uracil instead of thymine, from DNA as free bases. Copyright © 2015. Published by Elsevier B.V.

  10. BER Science Network Requirements

    Energy Technology Data Exchange (ETDEWEB)

    Alapaty, Kiran; Allen, Ben; Bell, Greg; Benton, David; Brettin, Tom; Canon, Shane; Dart, Eli; Cotter, Steve; Crivelli, Silvia; Carlson, Rich; Dattoria, Vince; Desai, Narayan; Egan, Richard; Tierney, Brian; Goodwin, Ken; Gregurick, Susan; Hicks, Susan; Johnston, Bill; de Jong, Bert; Kleese van Dam, Kerstin; Livny, Miron; Markowitz, Victor; McGraw, Jim; McCord, Raymond; Oehmen, Chris; Regimbal, Kevin; Shipman, Galen; Strand, Gary; Flick, Jeff; Turnbull, Susan; Williams, Dean; Zurawski, Jason

    2010-11-01

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the US Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In April 2010 ESnet and the Office of Biological and Environmental Research, of the DOE Office of Science, organized a workshop to characterize the networking requirements of the science programs funded by BER. The requirements identified at the workshop are summarized and described in more detail in the case studies and the Findings section. A number of common themes emerged from the case studies and workshop discussions. One is that BER science, like many other disciplines, is becoming more and more distributed and collaborative in nature. Another common theme is that data set sizes are exploding. Climate Science in particular is on the verge of needing to manage exabytes of data, and Genomics is on the verge of a huge paradigm shift in the number of sites with sequencers and the amount of sequencer data being generated.

  11. Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB

    Directory of Open Access Journals (Sweden)

    Joon-Ho Lee

    2014-09-01

    Full Text Available Genetics is important for breeding and selection of horses but there is a lack of well-established horse-related browsers or databases. In order to better understand horses, more variants and other integrated information are needed. Thus, we construct a horse genomic variants database including expression and other information. Horse Single Nucleotide Polymorphism and Expression Database (HSDB (http://snugenome2.snu.ac.kr/HSDB provides the number of unexplored genomic variants still remaining to be identified in the horse genome including rare variants by using population genome sequences of eighteen horses and RNA-seq of four horses. The identified single nucleotide polymorphisms (SNPs were confirmed by comparing them with SNP chip data and variants of RNA-seq, which showed a concordance level of 99.02% and 96.6%, respectively. Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants. The database will contribute to genetic improvement and breeding strategies of Thoroughbreds.

  12. Characterization of single nucleotide polymorphism markers for eelgrass (Zostera marina)

    NARCIS (Netherlands)

    Ferber, Steven; Reusch, Thorsten B. H.; Stam, Wytze T.; Olsen, Jeanine L.

    We characterized 37 single nucleotide polymorphism (SNP) makers for eelgrass Zostera marina. SNP markers were developed using existing EST (expressed sequence tag)-libraries to locate polymorphic loci and develop primers from the functional expressed genes that are deposited in The ZOSTERA database

  13. Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis

    Directory of Open Access Journals (Sweden)

    Suravajhala P

    2017-06-01

    Full Text Available Prashanth Suravajhala,1 Alfredo Benso2 1Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark; 2Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy Abstract: Next-generation sequencing technology has provided resources to easily explore and identify candidate single-nucleotide polymorphisms (SNPs and variants. However, there remains a challenge in identifying and inferring the causal SNPs from sequence data. A problem with different methods that predict the effect of mutations is that they produce false positives. In this hypothesis, we provide an overview of methods known for identifying causal variants and discuss the challenges, fallacies, and prospects in discerning candidate SNPs. We then propose a three-point classification strategy, which could be an additional annotation method in identifying causalities. Keywords: clinical mastitis, single-nucleotide polymorphisms, variants, associations, diseases, linkage disequilibrium, GWAS

  14. Synthesis, crystal structure, electrical properties, and sodium transport pathways of the new arsenate Na{sub 4}Co{sub 7}(AsO{sub 4}){sub 6}

    Energy Technology Data Exchange (ETDEWEB)

    Ben Smida, Youssef; Marzouki, Riadh [Université de Tunis El Manar, Laboratoire de Matériaux et Cristallochimie, Faculté des Sciences de Tunis, Campus Universitaire, 2092 Manar II, Tunis (Tunisia); Georges, Samuel [Université Grenoble Alpes, Laboratoire d’Electrochimie et de Physicochimie des Matériaux et des Interfaces LEPMI, F-38000 Grenoble (France); Kutteh, Ramzi [Bragg Institute, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, New South Wales 2234 (Australia); Avdeev, Maxim [Bragg Institute, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, New South Wales 2234 (Australia); School of Chemistry, University of Sydney, Sydney, New South Wales 2006 (Australia); Guesmi, Abderrahmen; Zid, Mohamed Faouzi [Université de Tunis El Manar, Laboratoire de Matériaux et Cristallochimie, Faculté des Sciences de Tunis, Campus Universitaire, 2092 Manar II, Tunis (Tunisia)

    2016-07-15

    A new sodium cobalt (II) arsenate Na{sub 4}Co{sub 7}(AsO{sub 4}){sub 6} has been synthesized by a solid-state reaction and its crystal structure determined from single crystal X-ray diffraction data. It crystallizes in the monoclinic system, space group C2/m, with a=10.7098(9) Å, b=14.7837(9) Å, c=6.6845(7) Å, and β=105.545(9)°. The structure is described as a three-dimensional framework built up of corner-edge sharing CoO{sub 6}, CoO{sub 4} and AsO{sub 4} polyhedra, with interconnecting channels along [100] in which the Na{sup +} cations are located. The densest ceramics with relative density of 94% was obtained by ball milling and optimization of sintering temperature, and its microstructure characterized by scanning electron microscopy. The electrical properties of the ceramics were studied over a temperature interval from 280 °C to 560 °C using the complex impedance spectroscopy over the range of 13 MHz–5 Hz. The ionic bulk conductivity value of the sample at 360 °C is 2.51 10{sup −5} S cm{sup −1} and the measured activation energy is Ea=1 eV. The sodium migration pathways in the crystal structure were investigated computationally using the bond valence site energy (BVSE) model and classical molecular dynamics (MD) simulations. - Graphical abstract: Correlation between crystal structure, microstructure and ionic conductivity . Display Omitted - Highlights: • A new arsenate Na{sub 4}Co{sub 7}(AsO{sub 4}){sub 6} was prepared by solid state reaction. • Its crystal structure was determined by powder X-ray diffraction. • Na{sup +} ionic conductivity was probed by complex impedance spectroscopy. • Na{sup +} conduction pathways were modeled by bond-valence method and molecular dynamics.

  15. Single nucleotide polymorphisms in the 5'-flanking region of the ...

    African Journals Online (AJOL)

    Prolactin (PRL), a polypeptide hormone synthesized and secreted by the animal's anterior pituitary gland, plays an important role in the regulation of mammalian lactation and avian reproduction. Considering the significant association between single nucleotide polymorphisms (SNPs) in the 5'-flanking region of PRL and ...

  16. 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.

  17. Assessment of single nucleotide polymorphisms in screening 52 DNA repair and cell cycle control genes in Fanconi anemia patients

    Directory of Open Access Journals (Sweden)

    Petrović Sandra

    2015-01-01

    Full Text Available Fanconi anemia (FA is a rare genetically heterogeneous disorder associated with bone marrow failure, birth defects and cancer susceptibility. Apart from the disease- causing mutations in FANC genes, the identification of specific DNA variations, such as single nucleotide polymorphisms (SNPs, in other candidate genes may lead to a better clinical description of this condition enabling individualized treatment with improvement of the prognosis. In this study, we have assessed 95 SNPs located in 52 key genes involved in base excision repair (BER, nucleotide excision repair (NER, mismatch repair (MMR, double strand break (DSB repair and cell cycle control using a DNA repair chip (Asper Biotech, Estonia which includes most of the common variants for the candidate genes. The SNP genotyping was performed in five FA-D2 patients and in one FA-A patient. The polymorphisms studied were synonymous (n=10, nonsynonymous (missense (n=52 and in non-coding regions of the genome (introns and 5 ‘and 3’ untranslated regions (UTR (n=33. Polymorphisms found at the homozygous state are selected for further analysis. Our results have shown a significant inter-individual variability among patients in the type and the frequency of SNPs and also elucidate the need for further studies of polymorphisms located in ATM, APEX APE 1, XRCC1, ERCC2, MSH3, PARP4, NBS1, BARD1, CDKN1B, TP53 and TP53BP1 which may be of great importance for better clinical description of FA. In addition, the present report recommends the use of SNPs as predictive and prognostic genetic markers to individualize therapy of FA patients. [Projekat Ministarstva nauke Republike Srbije, br. 173046

  18. Analysis of single nucleotide polymorphisms in case-control studies.

    Science.gov (United States)

    Li, Yonghong; Shiffman, Dov; Oberbauer, Rainer

    2011-01-01

    Single nucleotide polymorphisms (SNPs) are the most common type of genetic variants in the human genome. SNPs are known to modify susceptibility to complex diseases. We describe and discuss methods used to identify SNPs associated with disease in case-control studies. An outline on study population selection, sample collection and genotyping platforms is presented, complemented by SNP selection, data preprocessing and analysis.

  19. BER of subcarrier MPSK and MDPSK systems in atmospheric turbulence

    KAUST Repository

    Song, Xuegui

    2015-01-01

    Bit-error rate (BER) performance of subcarrier $M$-ary phase-shift keying (MPSK) and $M$-ary differential PSK (MDPSK) is analyzed for optical wireless communications over Gamma-Gamma and lognormal turbulence channels. We study the relation between the exact BER and the approximate BER, which is obtained by dividing the symbol-error rate by the number of bits per symbol, for subcarrier MPSK and MDPSK modulations. The asymptotic BER performance gap between the exact and the approximate BERs is quantified analytically through our asymptotic analyses. The accuracy of the approximate BER of both MPSK and MDPSK depends on the channel conditions. Under weak turbulence conditions, the approximate BER expression can be used to predict the system performance with high accuracy, while under strong turbulence conditions the approximate BER becomes inaccurate and can only serve as a loose lower bound of the exact BER. The asymptotic BER performance loss of MDPSK with respect to MPSK is also quantified analytically.

  20. Multiscale Computation. Needs and Opportunities for BER Science

    Energy Technology Data Exchange (ETDEWEB)

    Scheibe, Timothy D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Smith, Jeremy C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-01-01

    The Environmental Molecular Sciences Laboratory (EMSL), a scientific user facility managed by Pacific Northwest National Laboratory for the U.S. Department of Energy, Office of Biological and Environmental Research (BER), conducted a one-day workshop on August 26, 2014 on the topic of “Multiscale Computation: Needs and Opportunities for BER Science.” Twenty invited participants, from various computational disciplines within the BER program research areas, were charged with the following objectives; Identify BER-relevant models and their potential cross-scale linkages that could be exploited to better connect molecular-scale research to BER research at larger scales and; Identify critical science directions that will motivate EMSL decisions regarding future computational (hardware and software) architectures.

  1. Reducing BER of spectral-amplitude coding optical code-division multiple-access systems by single photodiode detection technique

    Science.gov (United States)

    Al-Khafaji, H. M. R.; Aljunid, S. A.; Amphawan, A.; Fadhil, H. A.; Safar, A. M.

    2013-03-01

    In this paper, we present a single photodiode detection (SPD) technique for spectral-amplitude coding optical code-division multiple-access (SAC-OCDMA) systems. The proposed technique eliminates both phase-induced intensity noise (PIIN) and multiple-access interference (MAI) in the optical domain. Analytical results show that for 35 simultaneous users transmitting at data rate of 622 Mbps, the bit-error rate (BER) = 1.4x10^-28 for SPD technique is much better compared to 9.3x10^-6 and 9.6x10^-3 for the modified-AND as well as the AND detection techniques, respectively. Moreover, we verified the improved performance afforded by the proposed technique using data transmission simulations.

  2. Kultur als Ordnungshypothese über Raum?

    OpenAIRE

    Klüter, Helmut

    2009-01-01

    Inhalt: 1 Einleitung 2 Zur Attraktivität von Kultur 3 Kulturologische Methodik 4 Schnittmengen mit und Bindearme zur Kulturgeographie 5 Kritische Argumente gegen Kultur als Ordnungshypothese über Raum 6 Räumliche Abstraktion als Ordnungsstrategie über „Kultur“? 7 Zusammenfassung

  3. Detection of new single nucleotide polymorphisms by means of real ...

    Indian Academy of Sciences (India)

    Unknown

    amplified millions to billions of times by means of a PCR before the PCR product ... Keywords. Single nucleotide polymorphism; real time PCR; DNA melting curve analysis. ... VAL158MET SNP and alcoholism and to test for interac- tions between the .... indicate a heterozygote sample (VAL/MET genotype). The curve with ...

  4. Hexagonal perovskites with cationic vacancies. 2. Ba/sub 8/Re/sub 2/W/sub 3/vacant/sub 3/O/sub 24/ - a novel hexagonal perovskite (24 L-type)

    Energy Technology Data Exchange (ETDEWEB)

    Kemmler-Sack, S [Tuebingen Univ. (Germany, F.R.). Inst. fuer Chemie

    1978-07-01

    The yellow Ba/sub 8/Re/sub 2/W/sub 3/vacant/sub 3/O/sub 24/ crystallizes in a rhombohedral layer structure of 24 L-type with a = 5.81/sub 3/ A; c = 55.52/sub 5/ A for the unit cell in trigonal setting and 3 formula units in the cell (rhosub(gef.) = 7.2/sub 6/ g/cm/sup 3/; rhosub(ber.) = 7.37/sub 8/ g/cm/sup 3/).

  5. The chlorophyll-deficient golden leaf mutation in cucumber is due to a single nucleotide substitution in CsChlI for magnesium chelatase I subunit.

    Science.gov (United States)

    Gao, Meiling; Hu, Liangliang; Li, Yuhong; Weng, Yiqun

    2016-10-01

    The cucumber chlorophyll-deficient golden leaf mutation is due to a single nucleotide substitution in the CsChlI gene for magnesium chelatase I subunit which plays important roles in the chlorophyll biosynthesis pathway. The Mg-chelatase catalyzes the insertion of Mg(2+) into the protoporphyrin IX in the chlorophyll biosynthesis pathway, which is a protein complex encompassing three subunits CHLI, CHLD, and CHLH. Chlorophyll-deficient mutations in genes encoding the three subunits have played important roles in understanding the structure, function and regulation of this important enzyme. In an EMS mutagenesis population, we identified a chlorophyll-deficient mutant C528 with golden leaf color throughout its development which was viable and able to set fruits and seeds. Segregation analysis in multiple populations indicated that this leaf color mutation was recessively inherited and the green color showed complete dominance over golden color. Map-based cloning identified CsChlI as the candidate gene for this mutation which encoded the CHLI subunit of cucumber Mg-chelatase. The 1757-bp CsChlI gene had three exons and a single nucleotide change (G to A) in its third exon resulted in an amino acid substitution (G269R) and the golden leaf color in C528. This mutation occurred in the highly conserved nucleotide-binding domain of the CHLI protein in which chlorophyll-deficient mutations have been frequently identified. The mutant phenotype, CsChlI expression pattern and the mutated residue in the CHLI protein suggested the mutant allele in C528 is unique among mutations identified so far in different species. This golden leaf mutant not only has its potential in cucumber breeding, but also provides a useful tool in understanding the CHLI function and its regulation in the chlorophyll biosynthesis pathway as well as chloroplast development.

  6. Heated oligonucleotide ligation assay (HOLA): an affordable single nucleotide polymorphism assay.

    Science.gov (United States)

    Black, W C; Gorrochotegui-Escalante, N; Duteau, N M

    2006-03-01

    Most single nucleotide polymorphism (SNP) detection requires expensive equipment and reagents. The oligonucleotide ligation assay (OLA) is an inexpensive SNP assay that detects ligation between a biotinylated "allele-specific detector" and a 3' fluorescein-labeled "reporter" oligonucleotide. No ligation occurs unless the 3' detector nucleotide is complementary to the SNP nucleotide. The original OLA used chemical denaturation and neutralization. Heated OLA (HOLA) instead uses a thermal stable ligase and cycles of denaturing and hybridization for ligation and SNP detection. The cost per genotype is approximately US$1.25 with two-allele SNPs or approximately US$1.75 with three-allele SNPs. We illustrate the development of HOLA for SNP detection in the Early Trypsin and Abundant Trypsin loci in the mosquito Aedes aegypti (L.) and at the a-glycerophosphate dehydrogenase locus in the mosquito Anopheles gambiae s.s.

  7. Approach to analysis of single nucleotide polymorphisms by automated constant denaturant capillary electrophoresis

    International Nuclear Information System (INIS)

    Bjoerheim, Jens; Abrahamsen, Torveig Weum; Kristensen, Annette Torgunrud; Gaudernack, Gustav; Ekstroem, Per O.

    2003-01-01

    Melting gel techniques have proven to be amenable and powerful tools in point mutation and single nucleotide polymorphism (SNP) analysis. With the introduction of commercially available capillary electrophoresis instruments, a partly automated platform for denaturant capillary electrophoresis with potential for routine screening of selected target sequences has been established. The aim of this article is to demonstrate the use of automated constant denaturant capillary electrophoresis (ACDCE) in single nucleotide polymorphism analysis of various target sequences. Optimal analysis conditions for different single nucleotide polymorphisms on ACDCE are evaluated with the Poland algorithm. Laboratory procedures include only PCR and electrophoresis. For direct genotyping of individual SNPs, the samples are analyzed with an internal standard and the alleles are identified by co-migration of sample and standard peaks. In conclusion, SNPs suitable for melting gel analysis based on theoretical thermodynamics were separated by ACDCE under appropriate conditions. With this instrumentation (ABI 310 Genetic Analyzer), 48 samples could be analyzed without any intervention. Several institutions have capillary instrumentation in-house, thus making this SNP analysis method accessible to large groups of researchers without any need for instrument modification

  8. The base excision repair pathway is required for efficient lentivirus integration.

    Directory of Open Access Journals (Sweden)

    Kristine E Yoder

    Full Text Available An siRNA screen has identified several proteins throughout the base excision repair (BER pathway of oxidative DNA damage as important for efficient HIV infection. The proteins identified included early repair factors such as the base damage recognition glycosylases OGG1 and MYH and the late repair factor POLß, implicating the entire BER pathway. Murine cells with deletions of the genes Ogg1, Myh, Neil1 and Polß recapitulate the defect of HIV infection in the absence of BER. Defective infection in the absence of BER proteins was also seen with the lentivirus FIV, but not the gammaretrovirus MMLV. BER proteins do not affect HIV infection through its accessory genes nor the central polypurine tract. HIV reverse transcription and nuclear entry appear unaffected by the absence of BER proteins. However, HIV integration to the host chromosome is reduced in the absence of BER proteins. Pre-integration complexes from BER deficient cell lines show reduced integration activity in vitro. Integration activity is restored by addition of recombinant BER protein POLß. Lentiviral infection and integration efficiency appears to depend on the presence of BER proteins.

  9. Single nucleotide polymorphisms in obesity-related genes and the risk of esophageal cancers.

    Science.gov (United States)

    Doecke, James D; Zhao, Zhen Zhen; Stark, Mitchell S; Green, Adèle C; Hayward, Nicholas K; Montgomery, Grant W; Webb, Penelope M; Whiteman, David C

    2008-04-01

    Rates of adenocarcinoma of the esophagus (EAC) and esophagogastric junction (EGJAC) have been rising rapidly in recent decades, in contrast to the declining rates of esophageal squamous cell carcinomas (ESCC). Obesity is a major risk factor for both EAC and EGJAC, but not ESCC, and there is speculation that obesity promotes adenocarcinoma development through endocrine and related pathways. We therefore compared the prevalence of 12 single nucleotide polymorphisms (SNPs) in nine candidate genes previously implicated in obesity pathways (LEP, LEPR, ADIPOQ, POMC, PPARalpha, PPARgamma, RXRgamma, GHRL, and INSIG2) in a large Australian case-control study comprising DNA samples from 260 EAC cases, 301 EGJAC cases, 213 ESCC cases, and 1,352 population controls. No SNPs were associated with EGJAC or ESCC. Although several SNPs seemed to be associated with EAC on crude analysis [ADIPOQ (rs1501299), LEP (5'-untranslated region), PPARgamma (H447H), and GHRL (M72L)], effect sizes were modest and none of the associations was significant after correcting for multiple comparisons. Further, we found no consistent evidence that any of the genotypes were associated with risk of EAC or EGJAC within strata of body mass index (30 kg/m(2)). In conclusion, our data suggest that these SNPs do not play a major role in esophageal carcinogenesis.

  10. Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology

    DEFF Research Database (Denmark)

    Pareek, Chandra Shekhar; Błaszczyk, Paweł; Dziuba, Piotr

    2017-01-01

    Background RNA-seq is a useful next-generation sequencing (NGS) technology that has been widely used to understand mammalian transcriptome architecture and function. In this study, a breed-specific RNA-seq experiment was utilized to detect putative single nucleotide polymorphisms (SNPs) in liver...

  11. BER Analysis of Coherent Free-Space Optical Communication Systems with a Focal-Plane-Based Wavefront Sensor

    Science.gov (United States)

    Cao, Jingtai; Zhao, Xiaohui; Liu, Wei; Gu, Haijun

    2018-03-01

    A wavefront sensor is one of most important units for an adaptive optics system. Based on our previous works, in this paper, we discuss the bit-error-rate (BER) performance of coherent free space optical communication systems with a focal-plane-based wavefront sensor. Firstly, the theory of a focal-plane-based wavefront sensor is given. Then the relationship between the BER and the mixing efficiency with a homodyne receiver is discussed on the basis of binary-phase-shift-keying (BPSK) modulation. Finally, the numerical simulation results are shown that the BER will be decreased obviously after aberrations correction with the focal-plane-based wavefront sensor. In addition, the BER will decrease along with increasing number of photons received within a single bit. These analysis results will provide a reference for the design of the coherent Free space optical communication (FSOC) system.

  12. A single nucleotide change affects fur-dependent regulation of sodB in H. pylori.

    Directory of Open Access Journals (Sweden)

    Beth M Carpenter

    Full Text Available Helicobacter pylori is a significant human pathogen that has adapted to survive the many stresses found within the gastric environment. Superoxide Dismutase (SodB is an important factor that helps H. pylori combat oxidative stress. sodB was previously shown to be repressed by the Ferric Uptake Regulator (Fur in the absence of iron (apo-Fur regulation [1]. Herein, we show that apo regulation is not fully conserved among all strains of H. pylori. apo-Fur dependent changes in sodB expression are not observed under iron deplete conditions in H. pylori strains G27, HPAG1, or J99. However, Fur regulation of pfr and amiE occurs as expected. Comparative analysis of the Fur coding sequence between G27 and 26695 revealed a single amino acid difference, which was not responsible for the altered sodB regulation. Comparison of the sodB promoters from G27 and 26695 also revealed a single nucleotide difference within the predicted Fur binding site. Alteration of this nucleotide in G27 to that of 26695 restored apo-Fur dependent sodB regulation, indicating that a single base difference is at least partially responsible for the difference in sodB regulation observed among these H. pylori strains. Fur binding studies revealed that alteration of this single nucleotide in G27 increased the affinity of Fur for the sodB promoter. Additionally, the single base change in G27 enabled the sodB promoter to bind to apo-Fur with affinities similar to the 26695 sodB promoter. Taken together these data indicate that this nucleotide residue is important for direct apo-Fur binding to the sodB promoter.

  13. Decay pathway and high-temperature luminescence of Eu{sup 3+} in Ca{sub 2}Gd{sub 8}Si{sub 6}O{sub 26}

    Energy Technology Data Exchange (ETDEWEB)

    Chambers, M.D. [Engineering Materials Department, College of Engineering, University of California, Santa Barbara, CA 93106-5050 (United States)], E-mail: chambers@engineering.ucsb.edu; Rousseve, P.A.; Clarke, D.R. [Engineering Materials Department, College of Engineering, University of California, Santa Barbara, CA 93106-5050 (United States)

    2009-03-15

    The temperature-dependent luminescence of Eu:Ca{sub 2}Gd{sub 8}Si{sub 6}O{sub 26} and its decay pathways are investigated in order to assess the utility of the material as a thermometric phosphor. Non-radiative decays are found to compete with radiative processes even at room temperature. A decay pathway involving decay through charge-transfer states is proposed based on the decay profiles of emissions from {sup 5}D{sub 1} and {sup 5}D{sub 0} levels and on the temperature sensitivity of the spectra as observed after excitation by several wavelengths. The implications of this on solid-state lighting are also discussed.

  14. RpoS plays a central role in the SOS induction by sub-lethal aminoglycoside concentrations in Vibrio cholerae.

    Science.gov (United States)

    Baharoglu, Zeynep; Krin, Evelyne; Mazel, Didier

    2013-01-01

    Bacteria encounter sub-inhibitory concentrations of antibiotics in various niches, where these low doses play a key role for antibiotic resistance selection. However, the physiological effects of these sub-lethal concentrations and their observed connection to the cellular mechanisms generating genetic diversification are still poorly understood. It is known that, unlike for the model bacterium Escherichia coli, sub-minimal inhibitory concentrations (sub-MIC) of aminoglycosides (AGs) induce the SOS response in Vibrio cholerae. SOS is induced upon DNA damage, and since AGs do not directly target DNA, we addressed two issues in this study: how sub-MIC AGs induce SOS in V. cholerae and why they do not do so in E. coli. We found that when bacteria are grown with tobramycin at a concentration 100-fold below the MIC, intracellular reactive oxygen species strongly increase in V. cholerae but not in E. coli. Using flow cytometry and gfp fusions with the SOS regulated promoter of intIA, we followed AG-dependent SOS induction. Testing the different mutation repair pathways, we found that over-expression of the base excision repair (BER) pathway protein MutY relieved this SOS induction in V. cholerae, suggesting a role for oxidized guanine in AG-mediated indirect DNA damage. As a corollary, we established that a BER pathway deficient E. coli strain induces SOS in response to sub-MIC AGs. We finally demonstrate that the RpoS general stress regulator prevents oxidative stress-mediated DNA damage formation in E. coli. We further show that AG-mediated SOS induction is conserved among the distantly related Gram negative pathogens Klebsiella pneumoniae and Photorhabdus luminescens, suggesting that E. coli is more of an exception than a paradigm for the physiological response to antibiotics sub-MIC.

  15. Pathway of /sup 14/Co/sub 2/ fixation in marine algae

    Energy Technology Data Exchange (ETDEWEB)

    Joshi, G V; Karekar, M D [Shivaji Univ., Kolhapur (India). Dept. of Botany

    1973-08-01

    Marine plants have a different metabolic environment which is likely to affect pathways of CO/sub 2/ fixation. It has been observed that in marine alga, Ulva lactuca, during short term light fixation of /sup 14/CO/sub 2/, besides PGA, an appreciable amount of activity was located in aspartate. This curious observation can now be explained on the basis of Hatch, Slack and Kortschak pathway of CO/sub 2/ fixation. In order to trace pathways of /sup 14/CO/sub 2/ in marine algae, a wide variety of algal specimens were exposed to NaH/sup 14/CO/sub 3/ in light and the products were analyzed. The algae selected were Ulva lactuca, Sargassum ilicifolium, Sphacelaria sp., Padina tetrastromatica, Chaetomorpha media and Enteromorpha tubulosa. It has been found that the pathways of CO/sub 2/ in the above marine algae differ from the conventional pattern recorded in Chlorella. The early labelling of aspartate and its subsequent utilization indicates that HSK pathway is operative in the marine algae. Malate synthesis is inhibited due to the effect of saline environment on the activity of malic dehydrogenase. Appreciable label in PGA is suggestive of the fact that Calvin and Bassham pathway as well as the HSK route are simultaneously operating. (auth)

  16. A STAT6 Intronic Single-Nucleotide Polymorphism is Associated with Clinical Malaria in Ghanaian Children

    Directory of Open Access Journals (Sweden)

    Daniel Amoako-Sakyi

    2016-01-01

    Full Text Available Malaria pathogenesis may be influenced by IgE responses and cytokine cross-regulation. Several mutations in the IL-4/STAT6 signaling pathway can alter cytokine cross-regulation and IgE responses during a Plasmodium falciparum malarial infection. This study investigated the relationship between a STAT6 intronic single-nucleotide polymorphism (rs3024974, total IgE, cytokines, and malaria severity in 238 Ghanaian children aged between 0.5 and 13 years. Total IgE and cytokine levels were measured by ELISA, while genotyping was done by polymerase chain reaction-restriction fragment length polymorphism (RFLP. Compared with healthy controls, heterozygosity protected against clinical malaria: uncomplicated malaria (odds ratios [OR] = 0.13, P < 0.001, severe malarial anemia (OR = 0.18, P < 0.001, and cerebral malaria (OR = 0.39, P = 0.022. Levels of total IgE significantly differed among malaria phenotypes (P = 0.044 and rs3024974 genotypes (P = 0.037. Neither cytokine levels nor IL-6/IL-10 ratios were associated with malaria phenotypes or rs3024974 genotypes. This study suggests a role for rs3024974 in malaria pathogenesis and offers further insights into an IL-4/STAT6 pathway mutation in malaria pathogenesis.

  17. Factor 11 single-nucleotide variants in women with heavy menstrual bleeding

    NARCIS (Netherlands)

    Wiewel-Verschueren, Sophie; Mulder, Andre B.; Meijer, Karina; Mulder, Rene

    2017-01-01

    In a previous study it was shown that lower factor XI (FXI) levels in women with heavy menstrual bleeding (HMB). Our aim was to determine the single-nucleotide variants (SNVs) in the F11 gene in women with HMB. In addition, an extensive literature search was performed to determine the clinical

  18. Tl{sub 10}Hg{sub 3}Cl{sub 16}: Single crystal growth, electronic structure and piezoelectric properties

    Energy Technology Data Exchange (ETDEWEB)

    Khyzhun, O.Y., E-mail: khyzhun@ipms.kiev.ua [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky Street, 03142 Kyiv (Ukraine); Piasecki, M. [Institute of Physics, J.Dlugosz University Częstochowa, Armii Krajowej 13/15, Częstochowa PL-42-217 (Poland); Kityk, I.V. [Electrical Engineering Department, Częstochowa University Technology, Armii Krajowej 17, PL-42-200 Częstochowa (Poland); Luzhnyi, I. [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky Street, 03142 Kyiv (Ukraine); Fedorchuk, A.O. [Department of Inorganic and Organic Chemistry, Lviv National University of Veterinary Medicine and Biotechnologies, 50 Pekarska Street, 79010 Lviv (Ukraine); Fochuk, P.M. [Yuriy Fed’kovych Chernivtsi National University, 2 Kotziubynskoho Street, 58012 Chernivtsi (Ukraine); Levkovets, S.I. [Department of Inorganic and Physical Chemistry, Lesya Ukrainka Eastern European National University, 13 Voli Avenue, 43025 Lutsk (Ukraine); Karpets, M.V. [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky Street, 03142 Kyiv (Ukraine); Parasyuk, O.V. [Department of Inorganic and Physical Chemistry, Lesya Ukrainka Eastern European National University, 13 Voli Avenue, 43025 Lutsk (Ukraine)

    2016-10-15

    Single crystal of the ternary halide Tl{sub 10}Hg{sub 3}Cl{sub 16} was grown using Bridgman-Stockbarger method. For the Tl{sub 10}Hg{sub 3}Cl{sub 16} crystal, we have measured X-ray photoelectron spectra for both pristine and Ar{sup +} ion-bombarded surfaces and additionally investigated photoinduced piezoelectricity. Our data indicate that the Tl{sub 10}Hg{sub 3}Cl{sub 16} single crystal surface is very sensitive with respect to Ar{sup +} ion-bombardment. In particular, Ar{sup +} ion-bombardment with energy of 3.0 keV over 5 min at an ion current density of 14 μA/cm{sup 2} causes significant changes of the elemental stoichiometry of the Tl{sub 10}Hg{sub 3}Cl{sub 16} surface resulting in an abrupt decrease of the mercury content in the top surface layers of the studied single crystal. As a result of the treatment, the mercury content becomes nil in the top surface layers. In addition, the present XPS measurements allow for concluding about very low hygroscopicity of the Tl{sub 10}Hg{sub 3}Cl{sub 16} single crystal surface. The property is extremely important for the crystal handling in optoelectronic or nano-electronic devices working at ambient conditions. The photoinduced piezoelectricity has been explored for Tl{sub 10}Hg{sub 3}Cl{sub 16} depending on nitrogen (λ=371 nm) laser power density and temperature. - Graphical abstract: As-grown single crystal boule of Tl{sub 10}Hg{sub 3}Cl{sub 16}; dependence of the effective piezoelecric coefficient d{sub 33} versus the photoinducing nitrogen laser power density, I, at different temperatures, T; and packing of the polyhedra of halide atoms around Hg atoms in the Tl{sub 10}Hg{sub 3}Cl{sub 16} structure. - Highlights: • High-quality Tl{sub 10}Hg{sub 3}Cl{sub 16} single crystal has been grown by Bridgman-Stockbarger method. • Electronic structure of Tl{sub 10}Hg{sub 3}Cl{sub 16} is studied by the XPS method. • Tl{sub 10}Hg{sub 3}Cl{sub 16} single crystal surface is sensitive with respect to Ar{sup +} ion

  19. Sirtuin 1 gene rs2273773 C >T single nucleotide polymorphism and ...

    African Journals Online (AJOL)

    Background: Sirtuin-1 (SIRT-1), a protein has been found to protect the cells against oxidative stress due to its deacetylase activity. In this investigation, we aimed to study SIRT-1 gene rs2273773 C >T single nucleotide polymorphism and markers of serum protein oxidation (protein carbonyl and sulfhydryl groups) in ...

  20. Identification of single nucleotide polymorphisms of the PI3K-AKT-mTOR pathway as a risk factor of central nervous system metastasis in metastatic breast cancer.

    Science.gov (United States)

    Le Rhun, Emilie; Bertrand, Nicolas; Dumont, Aurélie; Tresch, Emmanuelle; Le Deley, Marie-Cécile; Mailliez, Audrey; Preusser, Matthias; Weller, Michael; Revillion, Françoise; Bonneterre, Jacques

    2017-12-01

    The PI3K-AKT-mTOR pathway may be involved in the development of central nervous system (CNS) metastasis from breast cancer. Accordingly, herein we explored whether single nucleotide polymorphisms (SNPs) of this pathway are associated with altered risk of CNS metastasis formation in metastatic breast cancer patients. The GENEOM study (NCT00959556) included blood sample collection from breast cancer patients treated in the neoadjuvant, adjuvant or metastatic setting. We identified patients with CNS metastases for comparison with patients without CNS metastasis, defined as either absence of neurological symptoms or normal brain magnetic resonance imaging (MRI) before death or during 5-year follow-up. Eighty-eight SNPs of phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian (or mechanistic) target of rapamycin (mTOR) pathway genes were selected for analysis: AKT1 (17 SNPs), AKT2 (4), FGFR1 (2), mTOR (7), PDK1 (4), PI3KR1 (11), PI3KCA (20), PTEN (17), RPS6KB1 (6). Of 342 patients with metastases, 207 fulfilled the inclusion criteria: One-hundred-and-seven patients remained free of CNS metastases at last follow-up or date of death whereas 100 patients developed CNS metastases. Among clinical parameters, hormonal and human epidermal growth factor receptor-2 (HER2) status as well as vascular tumour emboli was associated with risk of CNS metastasis. Only PI3KR1-rs706716 was associated with CNS metastasis in univariate analysis after Bonferroni correction (p patients and could be included in a predictive composite score to detect early CNS metastasis irrespective of breast cancer subtype. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Microarray Beads for Identifying Blood Group Single Nucleotide Polymorphisms

    OpenAIRE

    Drago, Francesca; Karpasitou, Katerina; Poli, Francesca

    2009-01-01

    We have developed a high-throughput system for single nucleotide polymorphism (SNP) genotyping of alleles of diverse blood group systems exploiting Luminex technology. The method uses specific oligonucleotide probes coupled to a specific array of fluorescent microspheres and is designed for typing Jka/Jkb, Fya/Fyb, S/s, K/k, Kpa/Kpb, Jsa/Jsb, Coa/Cob and Lua/Lub alleles. Briefly, two multiplex PCR reactions (PCR I and PCR II) according to the laboratory specific needs are set up. PCR I amplif...

  2. Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

    Science.gov (United States)

    Holden, Todd; Tremberger, G., Jr.; Cheung, E.; Subramaniam, R.; Gadura, N.; Schneider, P.; Sullivan, R.; Flamholz, A.; Lieberman, D.; Cheung, T. D.

    2009-08-01

    The Single-Stranded DNA-Binding Protein (RPA) Genes in gamma ray radiation-resistant halophilic archaeon Halobacterium sp. NRC-1 were analyzed in terms of their nucleotide fluctuations. In an ATCG sequence, each base was assigned a number equal to its atomic number. The resulting numerical sequence was the basis of the statistical analysis in this study. Fractal analysis using the Higuchi method gave fractal dimensions of 2.04 and 2.06 for the gene sequences VNG2160 and VNG2162, respectively. The 16S rRNA sequence has a fractal dimension of 1.99. The di-nucleotide Shannon entropy values were found to be negatively correlated with the observed fractal dimensions (R2~ 0.992, N=3). Inclusion of Deinococcus radiodurans Rad-A in the regression analysis decreases the R2 slightly to 0.98 (N=4). A third VNG2163 RPA gene of unknown function but with upregulation activity under irradiation was found to have a fractal dimension of 2.05 and a Shannon entropy of 3.77 bits. The above results are similar to those found in bacterial Deinococcus radiodurans and suggest that their high radiation resistance property would have favored selection of CG di-nucleotide pairs. The two transcription factors TbpD (VNG7114) and TfbA (VNG 2184) were also studied. Using VNG7114, VNG2184, and VNG2163; the regression analysis of fractal dimension versus Shannon entropy shows that R2 ~ 0.997 for N =3. The VNG2163 unknown function may be related to the pathways with transcriptions closely regulated to sequences VNG7114 and VNG2184.

  3. Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA.

    Science.gov (United States)

    Khodakov, Dmitriy A; Khodakova, Anastasia S; Huang, David M; Linacre, Adrian; Ellis, Amanda V

    2015-03-04

    Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.

  4. Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms

    Science.gov (United States)

    Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to show the distribution of these 2 important incompatible cultivated pepper species. Estimated mean nucleotide...

  5. Optical fiber communication — An overview

    Indian Academy of Sciences (India)

    This paper deals with the historical development of optical communication systems and their failures initially. Then the different generations in optical fiber communication along with their features are discussed. Some aspects of total internal reflection, different types of fibers along with their size and refractive index profile, ...

  6. Targeted Metabolic Engineering Guided by Computational Analysis of Single-Nucleotide Polymorphisms (SNPs)

    DEFF Research Database (Denmark)

    Udatha, D B R K Gupta; Rasmussen, Simon; Sicheritz-Pontén, Thomas

    2013-01-01

    The non-synonymous SNPs, the so-called non-silent SNPs, which are single-nucleotide variations in the coding regions that give "birth" to amino acid mutations, are often involved in the modulation of protein function. Understanding the effect of individual amino acid mutations on a protein...

  7. Single crystal growth, magnetic and thermal properties of perovskite YFe{sub 0.6}Mn{sub 0.4}O{sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Tao [School of Materials Science and Engineering, Shanghai Institute of Technology, Shanghai 201418 (China); Synthetio Single Crystal Research Center, Shanghai Institute of Ceramic, Chinese Academy of Sciences, Shanghai 200050 (China); Key Laboratory of Transparent and Opto-functional Inorganic Materials, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Shen, Hui, E-mail: hshen@sit.edu.cn [School of Materials Science and Engineering, Shanghai Institute of Technology, Shanghai 201418 (China); Zhao, Xiangyang; Man, Peiwen [Synthetio Single Crystal Research Center, Shanghai Institute of Ceramic, Chinese Academy of Sciences, Shanghai 200050 (China); Key Laboratory of Transparent and Opto-functional Inorganic Materials, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Wu, Anhua, E-mail: wuanhua@mail.sic.ac.cn [Synthetio Single Crystal Research Center, Shanghai Institute of Ceramic, Chinese Academy of Sciences, Shanghai 200050 (China); Key Laboratory of Transparent and Opto-functional Inorganic Materials, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Su, Liangbi [Synthetio Single Crystal Research Center, Shanghai Institute of Ceramic, Chinese Academy of Sciences, Shanghai 200050 (China); Key Laboratory of Transparent and Opto-functional Inorganic Materials, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Xu, Jiayue, E-mail: xujiayue@sit.edu.cn [School of Materials Science and Engineering, Shanghai Institute of Technology, Shanghai 201418 (China)

    2016-11-01

    High quality YFe{sub 0.6}Mn{sub 0.4}O{sub 3} single crystal was grown by floating zone technique using a four-mirror-image-furnace under flowing air. Powder X-ray diffraction gives well evidence that the specimen has an orthorhombic structure, with space group Pbnm. Temperature dependence of the magnetizations of YFe{sub 0.6}Mn{sub 0.4}O{sub 3} single crystal were studied under ZFC and FC modes in the temperature range from 5 K to 400 K. A clear spin reorientation transition behavior (Γ{sub 4}→Γ{sub 1}) is observed in the temperature range of 322–316 K, due to the substitution of Mn at the Fe site of YFeO{sub 3}. Its Néel temperature is around 385 K. Moreover, the spin reorientation is verified by the change of magnetic hysteresis loops of the sample along [001] axis in the temperature range of 50–385 K. The thermal properties of the sample were measured by the differential scanning calorimeter (DSC) from 300 K to 500 K, which also clearly appear anomaly in the spin reorientation region. - Highlights: • High quality YFe{sub 0.6}Mn{sub 0.4}O{sub 3} single crystal was grown by floating zone technique. • The thermal properties appear anomaly in the spin reorientation region. • A clear spin reorientation transition behavior (Γ{sub 4}→Γ{sub 1}) is observed in the temperature range of 322–316 K, due to the substitution of Mn at the Fe site of YFeO{sub 3}.

  8. BER of subcarrier MPSK/MDPSK modulated OWC systems in Gamma-Gamma turbulence

    KAUST Repository

    Song, Xuegui

    2013-12-01

    Bit-error rate (BER) performance of subcarrier Mary phase-shift keying (MPSK) and M-ary differential PSK (MDPSK) is analyzed for optical wireless communications in Gamma-Gamma turbulence. We study the relation between the exact BER and the approximate BER, which is obtained by dividing the symbol error rate by the number of bits per symbol, for subcarrier MPSK and MDPSK modulations. The asymptotic performance gap between the exact and the approximate BERs is quantified analytically through our asymptotic analyses. The accuracy of the approximate BER of both MPSK and MDPSK depends on the channel conditions. Under weak turbulence conditions, the approximate BER expression can be used to predict the system performance with high accuracy, while under strong turbulence conditions the approximate BER becomes inaccurate and can only serve as a loose lower bound of the exact BER. The asymptotic BER performance loss of MDPSK with respect to MPSK is also quantified analytically. © 2013 IEEE.

  9. Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.).

    Science.gov (United States)

    Allen, Alexandra M; Barker, Gary L A; Berry, Simon T; Coghill, Jane A; Gwilliam, Rhian; Kirby, Susan; Robinson, Phil; Brenchley, Rachel C; D'Amore, Rosalinda; McKenzie, Neil; Waite, Darren; Hall, Anthony; Bevan, Michael; Hall, Neil; Edwards, Keith J

    2011-12-01

    Food security is a global concern and substantial yield increases in cereal crops are required to feed the growing world population. Wheat is one of the three most important crops for human and livestock feed. However, the complexity of the genome coupled with a decline in genetic diversity within modern elite cultivars has hindered the application of marker-assisted selection (MAS) in breeding programmes. A crucial step in the successful application of MAS in breeding programmes is the development of cheap and easy to use molecular markers, such as single-nucleotide polymorphisms. To mine selected elite wheat germplasm for intervarietal single-nucleotide polymorphisms, we have used expressed sequence tags derived from public sequencing programmes and next-generation sequencing of normalized wheat complementary DNA libraries, in combination with a novel sequence alignment and assembly approach. Here, we describe the development and validation of a panel of 1114 single-nucleotide polymorphisms in hexaploid bread wheat using competitive allele-specific polymerase chain reaction genotyping technology. We report the genotyping results of these markers on 23 wheat varieties, selected to represent a broad cross-section of wheat germplasm including a number of elite UK varieties. Finally, we show that, using relatively simple technology, it is possible to rapidly generate a linkage map containing several hundred single-nucleotide polymorphism markers in the doubled haploid mapping population of Avalon × Cadenza. © 2011 The Authors. Plant Biotechnology Journal © 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

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

    DEFF Research Database (Denmark)

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

    2003-01-01

    The genetic susceptibility to basal cell carcinoma (BCC) among Danish psoriatic patients was investigated in association studies with 12 single nucleotide polymorphisms on chromosome 19q13.2-3. The results show a significant association between BCC and the A-allele of a polymorphism in ERCCI exon4...

  11. Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations

    International Nuclear Information System (INIS)

    Kalari, Krishna R.; Rossell, David; Necela, Brian M.; Asmann, Yan W.; Nair, Asha

    2012-01-01

    KRAS mutations are highly prevalent in non-small cell lung cancer (NSCLC), and tumors harboring these mutations tend to be aggressive and resistant to chemotherapy. We used next-generation sequencing technology to identify pathways that are specifically altered in lung tumors harboring a KRAS mutation. Paired-end RNA-sequencing of 15 primary lung adenocarcinoma tumors (8 harboring mutant KRAS and 7 with wild-type KRAS) were performed. Sequences were mapped to the human genome, and genomic features, including differentially expressed genes, alternate splicing isoforms and single nucleotide variants, were determined for tumors with and without KRAS mutation using a variety of computational methods. Network analysis was carried out on genes showing differential expression (374 genes), alternate splicing (259 genes), and SNV-related changes (65 genes) in NSCLC tumors harboring a KRAS mutation. Genes exhibiting two or more connections from the lung adenocarcinoma network were used to carry out integrated pathway analysis. The most significant signaling pathways identified through this analysis were the NFκB, ERK1/2, and AKT pathways. A 27 gene mutant KRAS-specific sub network was extracted based on gene–gene connections from the integrated network, and interrogated for druggable targets. Our results confirm previous evidence that mutant KRAS tumors exhibit activated NFκB, ERK1/2, and AKT pathways and may be preferentially sensitive to target therapeutics toward these pathways. In addition, our analysis indicates novel, previously unappreciated links between mutant KRAS and the TNFR and PPARγ signaling pathways, suggesting that targeted PPARγ antagonists and TNFR inhibitors may be useful therapeutic strategies for treatment of mutant KRAS lung tumors. Our study is the first to integrate genomic features from RNA-Seq data from NSCLC and to define a first draft genomic landscape model that is unique to tumors with oncogenic KRAS mutations.

  12. Highly significant association between two common single nucleotide polymorphisms in CORIN gene and preeclampsia in Caucasian women.

    Directory of Open Access Journals (Sweden)

    Alain Stepanian

    Full Text Available Preeclampsia is a frequent medical complication during pregnancy. Corin, a serine protease which activates pro-atrial natriuretic peptide, has recently been shown to be involved in the pathophysiology of preeclampsia. The aim of this study was to search for CORIN gene variations and their association to preeclampsia in Caucasian and African women. Our study population was composed of 571 pregnant women (295 with preeclampsia and 276 normotensive controls matched for maternal and gestational age, and ethnic origin. The 22 exons of the CORIN gene were sequenced in a discovery sample (n = 260, where 31 single nucleotide polymorphisms were identified. In a replication sample (n = 311, 4 single nucleotide polymorphisms were tested. Two minor alleles (C for rs2271036 and G for rs2271037 were significantly associated to preeclampsia. Adjusted odds ratios [95% confidence interval] were 2.5 [1.2-3.8] (p = 0.007 and 2.3 [1.5-3.5] (p = 1.3 × 10(-4, respectively. These associations were ethnic-specific, as only found in the Caucasian of subjects (odds ratio = 3.5 [1.8-6.6], p = 1.1 × 10(-4; odds ratio = 3.1 [1.7-5.8], p = 2.1 × 10(-4, for each single nucleotide polymorphism, respectively. The two single nucleotide polymorphisms are in almost perfect linkage disequilibrium (r(2 = 0.93. No specific association was found with severe preeclampsia, early-onset preeclampsia nor fetal growth retardation. In conclusion, this is the first report of a highly significant association between these two single nucleotide polymorphisms in CORIN gene and preeclampsia. Our findings further support the probability of a critical role of corin in preeclamspia pathophysiology at the uteroplacental interface.

  13. Quasi-homoepitaxial growth of a-axis oriented PrBa sub 2 Cu sub 3 O sub 7 sub - subdelta thick film on (100) YBa sub 2 Cu sub 3 O sub 7 sub - subdelta single crystal

    CERN Document Server

    Sato, M; Morishita, T

    2003-01-01

    The structural characterizations of the quasi-homoepitaxial growth of a-axis oriented PrBa sub 2 Cu sub 3 O sub 7 sub - subdelta thick film grown on (100) YBa sub 2 Cu sub 3 O sub 7 sub - subdelta single crystal were investigated in comparison with those of the film grown on (001) YBa sub 2 Cu sub 3 O sub 7 sub - subdelta single crystal. The a-axis oriented PrBa sub 2 Cu sub 3 O sub 7 sub - subdelta films, expected to be a barrier layer, were prepared using a dc-95 MHz hybrid plasma sputtering on (100) and (001) YBa sub 2 Cu sub 3 O sub 7 sub - subdelta single crystals that are superconducting ground planes. The atomic force microscopy image revealed that the surfaces of 700-nm-thick a-axis PrBa sub 2 Cu sub 3 O sub 7 sub - subdelta films on (100) YBa sub 2 Cu sub 3 O sub 7 sub - subdelta single crystals were smooth with a mean roughness of 2.8 nm. X-ray diffraction scans showed that a-axis PrBa sub 2 Cu sub 3 O sub 7 sub - subdelta films deposited on (100) YBa sub 2 Cu sub 3 O sub 7 sub - subdelta single cry...

  14. Endothelial nitric oxide synthase single nucleotide polymorphism and left ventricular function in early chronic kidney disease.

    Directory of Open Access Journals (Sweden)

    Sourabh Chand

    Full Text Available Chronic kidney disease (CKD is associated with accelerated cardiovascular disease and heart failure. Endothelial nitric oxide synthase (eNOS Glu298Asp single nucleotide polymorphism (SNP genotype has been associated with a worse phenotype amongst patients with established heart failure and in patients with progression of their renal disease. The association of a cardiac functional difference in non-dialysis CKD patients with no known previous heart failure, and eNOS gene variant is investigated.140 non-dialysis CKD patients, who had cardiac magnetic resonance (CMR imaging and tissue doppler echocardiography as part of two clinical trials, were genotyped for eNOS Glu298Asp SNP retrospectively.The median estimated glomerular filtration rate (eGFR was 50 mls/min and left ventricular ejection fraction (LVEF was 74% with no overt diastolic dysfunction in this cohort. There were significant differences in LVEF across eNOS genotypes with GG genotype being associated with a worse LVEF compared to other genotypes (LVEF: GG 71%, TG 76%, TT 73%, p = 0.006. After multivariate analysis, (adjusting for age, eGFR, baseline mean arterial pressure, contemporary CMR heart rate, total cholesterol, high sensitive C-reactive protein, body mass index and gender GG genotype was associated with a worse LVEF, and increased LV end-diastolic and systolic index (p = 0.004, 0.049 and 0.009 respectively.eNOS Glu298Asp rs1799983 polymorphism in CKD patients is associated with relevant sub-clinical cardiac remodelling as detected by CMR. This gene variant may therefore represent an important genetic biomarker, and possibly highlight pathways for intervention, in these patients who are at particular risk of worsening cardiac disease as their renal dysfunction progresses.

  15. Distinct spatio temporal patterns and PARP dependence of XRCC1 recruitment to single-strand break and base excision repair

    International Nuclear Information System (INIS)

    Campalans, Anna; Kortulewski, Thierry; Amouroux, Rachel; Radicella, J. Pablo; Menoni, Herve; Vermeulen, Wim

    2013-01-01

    Single-strand break repair (SSBR) and base excision repair (BER) of modified bases and abasic sites share several players. Among them is XRCC1, an essential scaffold protein with no enzymatic activity, required for the coordination of both pathways. XRCC1 is recruited to SSBR by PARP-1, responsible for the initial recognition of the break. The recruitment of XRCC1 to BER is still poorly understood. Here we show by using both local and global induction of oxidative DNA base damage that XRCC1 participation in BER complexes can be distinguished from that in SSBR by several criteria. We show first that XRCC1 recruitment to BER is independent of PARP. Second, unlike SSBR complexes that are assembled within minutes after global damage induction, XRCC1 is detected later in BER patches, with kinetics consistent with the repair of oxidized bases. Third, while XRCC1-containing foci associated with SSBR are formed both in eu- and heterochromatin domains, BER complexes are assembled in patches that are essentially excluded from heterochromatin and where the oxidized bases are detected. (authors)

  16. Nucleotide Metabolism and its Control in Lactic Acid Bacteria

    DEFF Research Database (Denmark)

    Kilstrup, Mogens; Hammer, Karin; Jensen, Peter Ruhdal

    2005-01-01

    Most metabolic reactions are connected through either their utilization of nucleotides or their utilization of nucleotides or their regulation by these metabolites. In this review the biosynthetic pathways for pyrimidine and purine metabolism in lactic acid bacteria are described including...... the interconversion pathways, the formation of deoxyribonucleotides and the salvage pathways for use of exogenous precursors. The data for the enzymatic and the genetic regulation of these pathways are reviewed, as well as the gene organizations in different lactic acid bacteria. Mutant phenotypes and methods...... for manipulation of nucleotide pools are also discussed. Our aim is to provide an overview of the physiology and genetics of nucleotide metabolism and its regulation that will facilitate the interpretation of data arising from genetics, metabolomics, proteomics, and transcriptomics in lactic acid bacteria....

  17. Bi sub 2 Sr sub 2 Ca sub n sub - sub 1 Cu sub n O sub y films sputtered on substrates of Bi sub 2 Sr sub 2 CuO sub y single crystals

    CERN Document Server

    Katsurahara, K; Matsumoto, K; Fujiwara, N; Tanaka, H; Kishida, S

    2003-01-01

    We prepared Bi sub 2 Sr sub 2 CaCu sub 2 O sub y (Bi-2212) films on substrates of Bi sub 2 Sr sub 2 CuO sub y (Bi-2201) single crystals by a rf magnetron sputtering method, where He and O sub 2 mixture sputtering gas and an off-axis geometry were used. The EPMA measurement indicated that the films deposited on the Bi-2201 single crystal had approximately the same composition as those on MgO substrate, which showed a Bi-221 single-phase. The film deposited on the Bi-2201 single crystal post-annealed at 500degC for 0.5h showed a metallic temperature dependent resistance in the normal state and the superconducting transition (T sub c sup o sup n sup s sup e sup t) of about 80 K. Therefore, the Bi-2212 films are considerate to grow on the substrate of the Bi-2201 singe crystal. (author)

  18. Lupus-related single nucleotide polymorphisms and risk of diffuse large B-cell lymphoma

    NARCIS (Netherlands)

    Bernatsky, Sasha; Velásquez García, Héctor A; Spinelli, John; Gaffney, Patrick; Smedby, Karin E; Ramsey-Goldman, Rosalind; Wang, Sophia S.; Adami, Hans-Olov; Albanes, Demetrius; Angelucci, Emanuele; Ansell, Stephen M.; Asmann, Yan W.; Becker, Nikolaus; Benavente, Yolanda; Berndt, Sonja I.; Bertrand, Kimberly A.; Birmann, Brenda M.; Boeing, Heiner; Boffetta, Paolo; Bracci, Paige M.; Brennan, Paul; Brooks-Wilson, Angela R.; Cerhan, James R.; Chanock, Stephen J.; Clavel, Jacqueline; Conde, Lucia; Cotenbader, Karen H; Cox, David G; Cozen, Wendy; Crouch, Simon; De Roos, Anneclaire J.; De Sanjose, Silvia; Di Lollo, Simonetta; Diver, W. Ryan; Dogan, Ahmet; Foretova, Lenka; Ghesquières, Hervé; Giles, Graham G.; Glimelius, Bengt; Habermann, Thomas M.; Haioun, Corinne; Hartge, Patricia; Hjalgrim, Henrik; Holford, Theodore R.; Holly, Elizabeth A.; Jackson, Rebecca D.; Kaaks, Rudolph; Kane, Eleanor; Kelly, Rachel S.; Klein, Robert J.; Kraft, Peter; Kricker, Anne; Lan, Qing; Lawrence, Charles; Liebow, Mark; Lightfoot, Tracy; Link, Brian K.; Maynadie, Marc; McKay, James; Melbye, Mads; Molina, Thierry Jo; Monnereau, Alain; Morton, Lindsay M.; Nieters, Alexandra; North, Kari E.; Novak, Anne J.; Offit, Kenneth; Purdue, Mark P.; Rais, Marco; Riby, Jacques; Roman, Eve; Rothman, Nathaniel; Salles, Gilles; Severi, Gianluca; Severson, Richard K.; Skibola, Christine F.; Slager, Susan L.; Smith, Alex; Smith, Martyn T.; Southey, Melissa C.; Staines, Anthony; Teras, Lauren R.; Thompson, Carrie A.; Tilly, Hervé; Tinker, Lesley F.; Tjonneland, Anne; Turner, Jenny; Vajdic, Claire M.; Vermeulen, Roel C H; Vijai, Joseph; Vineis, Paolo; Virtamo, Jarmo; Wang, Zhaoming; Weinstein, Stephanie; Witzig, Thomas E.; Zelenetz, Andrew; Zeleniuch-Jacquotte, Anne; Zhang, Yawei; Zheng, Tongzhang; Zucca, Mariagrazia; Clarke, Ann E

    2017-01-01

    Objective: Determinants of the increased risk of diffuse large B-cell lymphoma (DLBCL) in SLE are unclear. Using data from a recent lymphoma genome-wide association study (GWAS), we assessed whether certain lupus-related single nucleotide polymorphisms (SNPs) were also associated with DLBCL.

  19. PCR/LDR/capillary electrophoresis for detection of single-nucleotide differences between fetal and maternal DNA in maternal plasma.

    Science.gov (United States)

    Yi, Ping; Chen, Zhuqin; Zhao, Yan; Guo, Jianxin; Fu, Huabin; Zhou, Yuanguo; Yu, Lili; Li, Li

    2009-03-01

    The discovery of fetal DNA in maternal plasma has opened up an approach for noninvasive diagnosis. We have now assessed the possibility of detecting single-nucleotide differences between fetal and maternal DNA in maternal plasma by polymerase chain reaction (PCR)/ligase detection reaction((LDR)/capillary electrophoresis. PCR/LDR/capillary electrophoresis was applied to detect the genotype of c.454-397T>gene (ESR1) from experimental DNA models of maternal plasma at different sensitivity levels and 13 maternal plasma samples.alphaC in estrogen receptor. (1) Our results demonstrated that the technique could discriminate low abundance single-nucleotide mutation with a mutant/normal allele ratio up to 1:10 000. (2) Examination of ESR1 c.454-397T>C genotypes by using the method of restriction fragment length analysis was performed in 25 pregnant women, of whom 13 pregnant women had homozygous genotypes. The c.454-397T>C genotypes of paternally inherited fetal DNA in maternal plasma of these 13 women were detected by PCR/LDR/capillary electrophoresis, which were accordant with the results of umbilical cord blood. PCR/LDR/capillary electrophoresis has very high sensitivity to distinguish low abundance single nucleotide differences and can discriminate point mutations and single-nucleotide polymorphisms(SNPs) of paternally inherited fetal DNA in maternal plasma.

  20. Single-nucleotide polymorphism of INS, INSR, IRS1, IRS2, PPAR-G ...

    Indian Academy of Sciences (India)

    2017-03-02

    Mar 2, 2017 ... Abstract. Polycystic ovary syndrome (PCOS) is the most common and a complex female endocrine disorder, and is one of the leading cause of female infertility. Here, we aimed to investigate the association of single-nucleotide polymorphism of INS, INSR,. IRS1, IRS2, PPAR-G and CAPN10 gene in the ...

  1. Single nucleotide polymorphism (SNP) detection on a magnetoresistive sensor

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Østerberg, Frederik Westergaard; Dufva, Martin

    2013-01-01

    We present a magnetoresistive sensor platform for hybridization assays and demonstrate its applicability on single nucleotide polymorphism (SNP) genotyping. The sensor relies on anisotropic magnetoresistance in a new geometry with a local negative reference and uses the magnetic field from...... the sensor bias current to magnetize magnetic beads in the vicinity of the sensor. The method allows for real-time measurements of the specific bead binding to the sensor surface during DNA hybridization and washing. Compared to other magnetic biosensing platforms, our approach eliminates the need...... for external electromagnets and thus allows for miniaturization of the sensor platform....

  2. Polychlorinated biphenyl quinone induces oxidative DNA damage and repair responses: The activations of NHEJ, BER and NER via ATM-p53 signaling axis

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Hui; Shi, Qiong; Song, Xiufang; Fu, Juanli; Hu, Lihua; Xu, Demei; Su, Chuanyang; Xia, Xiaomin; Song, Erqun; Song, Yang, E-mail: songyangwenrong@hotmail.com

    2015-07-01

    Our previous studies demonstrated that polychlorinated biphenyl (PCB) quinone induced oxidative DNA damage in HepG2 cells. To promote genomic integrity, DNA damage response (DDR) coordinates cell-cycle transitions, DNA repair and apoptosis. PCB quinone-induced cell cycle arrest and apoptosis have been documented, however, whether PCB quinone insult induce DNA repair signaling is still unknown. In this study, we identified the activation of DDR and corresponding signaling events in HepG2 cells upon the exposure to a synthetic PCB quinone, PCB29-pQ. Our data illustrated that PCB29-pQ induces the phosphorylation of p53, which was mediated by ataxia telangiectasia mutated (ATM) protein kinase. The observed phosphorylated histone H2AX (γ-H2AX) foci and the elevation of 8-hydroxy-2′-deoxyguanosine (8-OHdG) indicated that DDR was stimulated by PCB29-pQ treatment. Additionally, we found PCB29-pQ activates non-homologous end joining (NHEJ), base excision repair (BER) and nucleotide excision repair (NER) signalings. However, these repair pathways are not error-free processes and aberrant repair of DNA damage may cause the potential risk of carcinogenesis and mutagenesis. - Highlights: • Polychlorinated biphenyl quinone induces oxidative DNA damage in HepG2 cells. • The elevation of γ-H2AX and 8-OHdG indicates the activation of DNA damage response. • ATM-p53 signaling acts as the DNA damage sensor and effector. • Polychlorinated biphenyl quinone activates NHEJ, BER and NER signalings.

  3. A Nucleotide Phosphatase Activity in the Nucleotide Binding Domain of an Orphan Resistance Protein from Rice*

    Science.gov (United States)

    Fenyk, Stepan; de San Eustaquio Campillo, Alba; Pohl, Ehmke; Hussey, Patrick J.; Cann, Martin J.

    2012-01-01

    Plant resistance proteins (R-proteins) are key components of the plant immune system activated in response to a plethora of different pathogens. R-proteins are P-loop NTPase superfamily members, and current models describe their main function as ATPases in defense signaling pathways. Here we show that a subset of R-proteins have evolved a new function to combat pathogen infection. This subset of R-proteins possesses a nucleotide phosphatase activity in the nucleotide-binding domain. Related R-proteins that fall in the same phylogenetic clade all show the same nucleotide phosphatase activity indicating a conserved function within at least a subset of R-proteins. R-protein nucleotide phosphatases catalyze the production of nucleoside from nucleotide with the nucleotide monophosphate as the preferred substrate. Mutation of conserved catalytic residues substantially reduced activity consistent with the biochemistry of P-loop NTPases. Kinetic analysis, analytical gel filtration, and chemical cross-linking demonstrated that the nucleotide-binding domain was active as a multimer. Nuclear magnetic resonance and nucleotide analogues identified the terminal phosphate bond as the target of a reaction that utilized a metal-mediated nucleophilic attack by water on the phosphoester. In conclusion, we have identified a group of R-proteins with a unique function. This biochemical activity appears to have co-evolved with plants in signaling pathways designed to resist pathogen attack. PMID:22157756

  4. A nucleotide phosphatase activity in the nucleotide binding domain of an orphan resistance protein from rice.

    Science.gov (United States)

    Fenyk, Stepan; Campillo, Alba de San Eustaquio; Pohl, Ehmke; Hussey, Patrick J; Cann, Martin J

    2012-02-03

    Plant resistance proteins (R-proteins) are key components of the plant immune system activated in response to a plethora of different pathogens. R-proteins are P-loop NTPase superfamily members, and current models describe their main function as ATPases in defense signaling pathways. Here we show that a subset of R-proteins have evolved a new function to combat pathogen infection. This subset of R-proteins possesses a nucleotide phosphatase activity in the nucleotide-binding domain. Related R-proteins that fall in the same phylogenetic clade all show the same nucleotide phosphatase activity indicating a conserved function within at least a subset of R-proteins. R-protein nucleotide phosphatases catalyze the production of nucleoside from nucleotide with the nucleotide monophosphate as the preferred substrate. Mutation of conserved catalytic residues substantially reduced activity consistent with the biochemistry of P-loop NTPases. Kinetic analysis, analytical gel filtration, and chemical cross-linking demonstrated that the nucleotide-binding domain was active as a multimer. Nuclear magnetic resonance and nucleotide analogues identified the terminal phosphate bond as the target of a reaction that utilized a metal-mediated nucleophilic attack by water on the phosphoester. In conclusion, we have identified a group of R-proteins with a unique function. This biochemical activity appears to have co-evolved with plants in signaling pathways designed to resist pathogen attack.

  5. Results from the first single cell Nb<sub>3sub>Sn cavity coatings at JLab

    Energy Technology Data Exchange (ETDEWEB)

    Eremeev, Grigory [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2015-09-01

    Nb<sub>3sub>Sn is a promising superconducting material for SRF applications and has the potential to exceed the limitations of niobium. We have used the recently commissioned Nb<sub>3sub>Sn coating system to investigate Nb<sub>3sub>Sn coatings on several single cell cavities by applying the same coating procedure on several different single cells with different history and pre-coating surface preparation. We report on our findings with four 1.5 GHz CEBAF-shape single cell and one 1.3 GHz ILC-shape single cavities that were coated, inspected, and tested.

  6. Assessment of Genetic Diversity in Faba Bean Based on Single Nucleotide Polymorphism

    Directory of Open Access Journals (Sweden)

    Sukhjiwan Kaur

    2014-01-01

    Full Text Available Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L. genotypes was evaluated for intra- and inter-population diversity using a set of 768 genome-wide distributed single nucleotide polymorphism (SNP markers, of which 657 obtained successful amplification and detected polymorphisms. Gene diversity and polymorphism information content (PIC values varied between 0.022–0.500 and 0.023–1.00, with averages of 0.363 and 0.287, respectively. The genetic structure of the germplasm collection was analysed and a neighbour-joining (NJ dendrogram was constructed. The faba bean accessions grouped into two major groups, with several additional smaller sub-groups, predominantly on the basis of geographical origin. These results were further supported by principal co-ordinate analysis (PCoA, deriving two major groupings which were differentiated on the basis of site of origin and pedigree relationships. In general, high levels of heterozygosity were observed, presumably due to the partially allogamous nature of the species. The results will facilitate targeted crossing strategies in future faba bean breeding programs in order to achieve genetic gain.

  7. Electron spin resonance study of a La sub 0 sub . sub 7 Ca sub 0 sub . sub 3 MnO sub 3 single crystal

    CERN Document Server

    Joh, K W; Lee, C E; Hur, N H; Ri, H C

    2003-01-01

    Comprehensive measurements of electron spin resonance were carried out on a La sub 0 sub . sub 7 Ca sub 0 sub . sub 3 MnO sub 3 single crystal over a wide temperature range covering the ferromagnetic as well as the paramagnetic phases. Our analysis of the asymmetric lineshapes indicates that the phase segregation of good and poor conducting regions persists far above the ferromagnetic-paramagnetic phase transition temperature.

  8. BER and FER Prediction of Control and Traffic Channels for a GSM type of interface

    DEFF Research Database (Denmark)

    Wigard, Jeroen; Nielsen, Thomas Toftegaard; Michaelsen, Per Henrik

    1998-01-01

    in a network simulator, but without having to simulate every single link, since this would be to time consuming. In this paper a method is presented to find the BER and FER from the signal to interference (C/I) values for a GSM type of air-interface, which can be used for integration of link aspects...... in a network simulator. The accuracy is within 0.2 dB in case of the BER and 0.5 for the FER. Both traffic and control channels are studied and the method is independent of hopping sequences and speed...

  9. A Lateral Flow Biosensor for the Detection of Single Nucleotide Polymorphisms.

    Science.gov (United States)

    Zeng, Lingwen; Xiao, Zhuo

    2017-01-01

    A lateral flow biosensor (LFB) is introduced for the detection of single nucleotide polymorphisms (SNPs). The assay is composed of two steps: circular strand displacement reaction and lateral flow biosensor detection. In step 1, the nucleotide at SNP site is recognized by T4 DNA ligase and the signal is amplified by strand displacement DNA polymerase, which can be accomplished at a constant temperature. In step 2, the reaction product of step 1 is detected by a lateral flow biosensor, which is a rapid and cost effective tool for nuclei acid detection. Comparing with conventional methods, it requires no complicated machines. It is suitable for the use of point of care diagnostics. Therefore, this simple, cost effective, robust, and promising LFB detection method of SNP has great potential for the detection of genetic diseases, personalized medicine, cancer related mutations, and drug-resistant mutations of infectious agents.

  10. Enhanced photoactivity from single-crystalline SrTaO{sub 2}N nanoplates synthesized by topotactic nitridation

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Jie; Skrabalak, Sara E. [Department of Chemistry, Indiana University, Bloomington, IN (United States)

    2017-11-06

    There are few methods yielding oxynitride crystals with defined shape, yet shape-controlled crystals often give enhanced photoactivity. Herein, single-crystalline SrTaO{sub 2}N nanoplates and polyhedra are achieved selectively. Central to these synthetic advances is the crystallization pathways used, in which single-crystalline SrTaO{sub 2}N nanoplates form by topotactic nitridation of aerosol-prepared Sr{sub 2}Ta{sub 2}O{sub 7} nanoplates and SrTaO{sub 2}N polyhedra form by flux-assisted nitridation of the nanoplates. Evaluation of these materials for the oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) showed improved performance for the SrTaO{sub 2}N nanoplates, with a record apparent quantum efficiency (AQE) of 6.1 % for OER compared to the polyhedra (AQE: 1.6 %) and SrTaO{sub 2}N polycrystals (AQE: 0.6 %). The enhanced performance from the nanoplates arises from their morphology and lower defect density. These results highlight the importance of developing new synthetic routes to high quality oxynitrides. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  11. Moessbauer studies of single crystal Pr sub 1 sub / sub 3 Sr sub 2 sub / sub 3 FeO sub 3

    CERN Document Server

    Uhm, Y R; Kim, C S; Tomioka, Y; Tokura, Y

    2000-01-01

    Single crystal Pr sub 1 sub / sub 3 Sr sub 2 sub / sub 3 FeO sub 3 was synthesized by using the floating zone method and the relation of magnetic properties and charge ordering transition with lattice dynamics was systematically investigated. Moessbauer spectra of Pr sub 1 sub / sub 3 sub S r sub 2 sub / sub 3 FeO sub 3 were taken at various temperatures ranging from 20 K to room temperature. The charge disproportionation, in which iron with valence states Fe sup 3 sup + and Fe sup 5 sup + was found in a ratio of 2:1, was detected in Pr sub 1 sub / sub 3 Sr sub 2 sub / sub 3 FeO sub 3 below 190+-3 K. Iron with valence state Fe sup 4 sup + coexisted in Pr sub 1 sub / sub 3 sub S r sub 2 sub / sub 3 FeO sub 3 at and above 150 K, and its ratio increased from 13 to 66 % with increasing temperature. This result means that charge-ordered and -disordered phases co-exist in Pr sub 1 sub / sub 3 Sr sub 2 sub / sub 3 FeO sub 3.

  12. The seeding effect of floating zone growth on Nd sub 1 sub . sub 8 sub 5 Ce sub 0 sub . sub 1 sub 5 CuO sub 4 and Bi sub 2 Sr sub 2 CaCu sub 2 O sub 8 sub - subdelta single crystals

    CERN Document Server

    Lin, C T; Liang, B

    2002-01-01

    Single crystals with the [100] orientation were selected and used as seeds to investigate the effect of travelling solvent floating zone growth on superconducting oxides of Nd sub 1 sub . sub 8 sub 5 Ce sub 0 sub . sub 1 sub 5 CuO sub 4 and Bi sub 2 Sr sub 2 CaCu sub 2 O sub 8 sub - subdelta. The number of nuclei was remarkably reduced and random nuclei could be eased when the seeding was applied during the growth of Nd sub 1 sub . sub 8 sub 5 Ce sub 0 sub . sub 1 sub 5 CuO sub 4 single crystals, compared to the crystals grown without seed. The crystal could preferentially grow on the seed although some additional nuclei occurred at the solid-liquid interface during the initial growth process. In consequence, the crystal ingot obtained is a large single grain having dimensions of 5 mm in diameter and 40 mm in length. The orientation of the seeded growth crystal was found to be 5deg off the [100] seed identified by an x-ray Laue pattern. For the growth of Bi sub 2 Sr sub 2 CaCu sub 2 O sub 8 sub - subdelta, it...

  13. [Meta-analysis on relationship between single nucleotide polymorphism of rs2231142 in ABCG2 gene and gout in East Asian population].

    Science.gov (United States)

    Wu, Lei; He, Yao; Zhang, Di

    2015-11-01

    To systematically evaluate the association between single nucleotide polymorphism of rs2231142 genetic susceptibility and gout in East Asian population. The literature retrieval was conducted by using English databases (Medline, EMbase), Chinese databases (CNKI, Vip, Wanfang, SinaMed) and others to collect the published papers on the association between single nucleotide polymorphism of rs2231142 genetic susceptibility and gout by the end of December 2014. Meta-analysis was performed with software Stata 12.0. Nine studies were included. There were significant associations between increased risk of gout and single nucleotide polymorphism of rs2231142, the combined OR was 2.04 (95%CI: 1.82-2.28) for A allele and C allele, 1.97 (95%CI: 1.57-2.48) for CA and CC, 3.71 (95%CI: 3.07-4.47) for AA and CC. Sex and region specific subgroup analysis showed less heterogeneity. There is significant association between gout and single nucleotide polymorphism of rs2231142 in East Asian population, and A allele is a high risk gene for gout.

  14. Electrical transport properties study of Mo{sub 0.6}W{sub 0.4}Se{sub 2} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Chaki, Sunil; Deshpande, M. P.; Tailor, J. P.; Chaudhary, M. D.; Sakaria, Pallavi N. [Department of Physics, Sardar Patel University, Vallabh Vidyanagar, Gujarat-388120 (India)

    2012-06-05

    The mixed transition metal dichalcogenide single crystals Mo{sub 0.6}W{sub 0.4}Se{sub 2} were characterized employing EDAX (Energy Dispersive Analysis of X-ray), (XRD) X-ray diffraction, SEM (Scanning Electron Microscope) and UV-Vis-NIR spectroscopy techniques. The electrical transport properties of as-grown Mo{sub 0.6}W{sub 0.4}Se{sub 2} single crystals were studied by two probe d. c. resistivity, Hall Effect and thermoelectric power measurement set-up. The obtained results are discussed in details.

  15. Single Nucleotide Polymorphisms in IL1B and the Risk of Acute Coronary Syndrome: A Danish Case-Cohort Study

    DEFF Research Database (Denmark)

    Stegger, Jakob Gerhard; Schmidt, Erik Berg; Tjonneland, Anne

    2012-01-01

    Background: Interleukin-1B (IL-1B) is a key pro-inflammatory cytokine that has been associated with the development of atherosclerosis and myocardial infarction. However, the prospective associations between functional single nucleotide polymorphisms (SNPs) in IL1B and incident acute coronary...... and 234 women). All cases were validated by review of medical records, and information on covariates was collected by study technicians. The study was conducted according to a case-cohort study design including ACS cases and a sex-stratified sub cohort of 1663 participants drawn randomly from the entire...... IL1B haplotypes and risk factors, respectively. Conclusions/Significance: Genetic variation in the promoter region of IL1B may not be associated with incident ACS in men or women above the age of 50 years....

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  17. Sirtuin1 single nucleotide polymorphism (A2191G is a diagnostic marker for vibration-induced white finger disease

    Directory of Open Access Journals (Sweden)

    Voelter-Mahlknecht Susanne

    2012-10-01

    Full Text Available Abstract Background Vibration-induced white finger disease (VWF, also known as hand-arm vibration syndrome, is a secondary form of Raynaud’s disease, affecting the blood vessels and nerves. So far, little is known about the pathogenesisof the disease. VWF is associated with an episodic reduction in peripheral blood flow. Sirtuin 1, a class III histone deacetylase, has been described to regulate the endothelium dependent vasodilation by targeting endothelial nitric oxide synthase. We assessed Sirt1single nucleotide polymorphisms in patients with VWF to further elucidate the role of sirtuin 1 in the pathogenesis of VWF. Methods Peripheral blood samples were obtained from 74 patients with VWF (male 93.2%, female 6.8%, median age 53 years and from 317 healthy volunteers (gender equally distributed, below 30 years of age. Genomic DNA was extracted from peripheral blood mononuclear cells and screened for potential Sirt1single nucleotide polymorphisms. Four putative genetic polymorphisms out of 113 within the Sirt1 genomic region (NCBI Gene Reference: NM_012238.3 were assessed. Allelic discrimination was performed by TaqMan-polymerasechainreaction-based allele-specific genotyping single nucleotide polymorphism assays. Results Sirt1single nucleotide polymorphism A2191G (Assay C_25611590_10, rs35224060 was identified within Sirt1 exon 9 (amino acid position 731, Ile → Val, with differing allelic frequencies in the VWF population (A/A: 70.5%, A/G: 29.5%, G/G: 0% and the control population (A/A: 99.7%, A/G: 0.3%, G/G: 0.5%, with significance levels of P U test (two-tailed P t-test and Chi-square test with Yates correction (all two-tailed: P Conclusion We identified theSirt1A2191Gsingle nucleotide polymorphism as a diagnostic marker for VWF.

  18. Flexibility of the myosin heavy chain: direct evidence that the region containing SH/sub 1/ and SH/sub 2/ can move 10 /Angstrom/ under the influence of nucleotide binding

    Energy Technology Data Exchange (ETDEWEB)

    Huston, E.E.; Grammer, J.C.; Yount, R.G.

    1988-12-13

    Previous experiments demonstrated that two thiols of skeletal myosin subfragment 1 (SF/sub 1/) could be oxidized to a disulfide bond by treatment with a 2-fold excess of 5,5'-dithiobis (2-nitrobenzoic acid) (DTNB) in the presence of MgADP. The resulting characteristic changes in the ATPase activities of SF/sub 1/ and the fact that MgADP was stably trapped at the active site, suggested that the two thiols cross-linked were SH/sub 1/ (Cys-707) and SH/sub 2/ (Cys-697) from the myosin heavy chain. To verify this suggestion, SF/sub 1/, after DTNB treatment as above, was treated with an excess of N-ethylmaleimide to block all accessible thiols. The single protein disulfide produced by DTNB oxidation was reduced with dithioerythritol and the modified SF/sub 1/ internally cross-linked with equimolar (/sup 14/C)p-phenylenedimaleimide (pPDM) in the presence of MgADP. After extensive trypsinization, the major /sup 14/C-labeled peptide was isolated, characterized, and shown to be Cys-Asn-Gly-Val-Leu-Gly-Ile-Arg-Ile-Cys-Arg, in which the two cysteines were cross-linked by pPDM. This peptide is known to contain SH/sub 2/ and SH/sub 1/ in this order and to come from residues 697-708 in the rabbit skeletal myosin heavy chain. Parallel experiments with (/sup 14/C)pPDM and unmodified SF/sub 1/ similar to those above gave an identical SH/sub 1/, SH/sub 2/ tryptic peptide, verifying earlier labeling results. These combined results demonstrate that SH/sub 1/ and SH/sub 2/ cross-linked by pPDM (12-13 /Angstrom/, S to S) or by oxidation with DTNB (2 /Angstrom/, S to S) can move a minimum of 10 /Angstrom/ under the influence of nucleotide binding. Because these residues are separated by only nine amino acids in the primary sequence, this small section of the heavy chain must possess extraordinary flexibility.

  19. The low single nucleotide polymorphism heritability of plasma and saliva cortisol levels.

    Science.gov (United States)

    Neumann, Alexander; Direk, Nese; Crawford, Andrew A; Mirza, Saira; Adams, Hieab; Bolton, Jennifer; Hayward, Caroline; Strachan, David P; Payne, Erin K; Smith, Jennifer A; Milaneschi, Yuri; Penninx, Brenda; Hottenga, Jouke J; de Geus, Eco; Oldehinkel, Albertine J; van der Most, Peter J; de Rijke, Yolanda; Walker, Brian R; Tiemeier, Henning

    2017-11-01

    Cortisol is an important stress hormone affected by a variety of biological and environmental factors, such as the circadian rhythm, exercise and psychological stress. Cortisol is mostly measured using blood or saliva samples. A number of genetic variants have been found to contribute to cortisol levels with these methods. While the effects of several specific single genetic variants is known, the joint genome-wide contribution to cortisol levels is unclear. Our aim was to estimate the amount of cortisol variance explained by common single nucleotide polymorphisms, i.e. the SNP heritability, using a variety of cortisol measures, cohorts and analysis approaches. We analyzed morning plasma (n=5705) and saliva levels (n=1717), as well as diurnal saliva levels (n=1541), in the Rotterdam Study using genomic restricted maximum likelihood estimation. Additionally, linkage disequilibrium score regression was fitted on the results of genome-wide association studies (GWAS) performed by the CORNET consortium on morning plasma cortisol (n=12,597) and saliva cortisol (n=7703). No significant SNP heritability was detected for any cortisol measure, sample or analysis approach. Point estimates ranged from 0% to 9%. Morning plasma cortisol in the CORNET cohorts, the sample with the most power, had a 6% [95%CI: 0-13%] SNP heritability. The results consistently suggest a low SNP heritability of these acute and short-term measures of cortisol. The low SNP heritability may reflect the substantial environmental and, in particular, situational component of these cortisol measures. Future GWAS will require very large sample sizes. Alternatively, more long-term cortisol measures such as hair cortisol samples are needed to discover further genetic pathways regulating cortisol concentrations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Mittheilungen über Scyphomedusen I

    NARCIS (Netherlands)

    Stiasny, G.

    1921-01-01

    Hiemit beabsichtige ich eine Reihe kleinerer Mittheilungen über Semaeostomeen und Rhizostomeen des Rijksmuseums van Natuurlijke Historie in Leiden zu veröffentlichen, welche die Systematik, Biologie, Entwicklungsgeschichte und Anatomie verschiedener Scyphomedusen behandeln. Die vorliegenden beiden

  1. SNR and BER Models and the Simulation for BER Performance of Selected Spectral Amplitude Codes for OCDMA

    Directory of Open Access Journals (Sweden)

    Abdul Latif Memon

    2014-01-01

    Full Text Available Many encoding schemes are used in OCDMA (Optical Code Division Multiple Access Network but SAC (Spectral Amplitude Codes is widely used. It is considered an effective arrangement to eliminate dominant noise called MAI (Multi Access Interference. Various codes are studied for evaluation with respect to their performance against three noises namely shot noise, thermal noise and PIIN (Phase Induced Intensity Noise. Various Mathematical models for SNR (Signal to Noise Ratios and BER (Bit Error Rates are discussed where the SNRs are calculated and BERs are computed using Gaussian distribution assumption. After analyzing the results mathematically, it is concluded that ZCC (Zero Cross Correlation Code performs better than the other selected SAC codes and can serve larger number of active users than the other codes do. At various receiver power levels, analysis points out that RDC (Random Diagonal Code also performs better than the other codes. For the power interval between -10 and -20 dBm performance of RDC is better ZCC. Their lowest BER values suggest that these codes should be part of an efficient and cost effective OCDM access network in the future.

  2. From Single Nucleotide Polymorphisms to Constant Immunosuppression: Mesenchymal Stem Cell Therapy for Autoimmune Diseases

    Directory of Open Access Journals (Sweden)

    Raghavan Chinnadurai

    2013-01-01

    Full Text Available The regenerative abilities and the immunosuppressive properties of mesenchymal stromal cells (MSCs make them potentially the ideal cellular product of choice for treatment of autoimmune and other immune mediated disorders. Although the usefulness of MSCs for therapeutic applications is in early phases, their potential clinical use remains of great interest. Current clinical evidence of use of MSCs from both autologous and allogeneic sources to treat autoimmune disorders confers conflicting clinical benefit outcomes. These varied results may possibly be due to MSC use across wide range of autoimmune disorders with clinical heterogeneity or due to variability of the cellular product. In the light of recent genome wide association studies (GWAS, linking predisposition of autoimmune diseases to single nucleotide polymorphisms (SNPs in the susceptible genetic loci, the clinical relevance of MSCs possessing SNPs in the critical effector molecules of immunosuppression is largely undiscussed. It is of further interest in the allogeneic setting, where SNPs in the target pathway of MSC's intervention may also modulate clinical outcome. In the present review, we have discussed the known critical SNPs predisposing to disease susceptibility in various autoimmune diseases and their significance in the immunomodulatory properties of MSCs.

  3. Complex DNA repair pathways as possible therapeutic targets to overcome temozolomide resistance in glioblastoma

    International Nuclear Information System (INIS)

    Yoshimoto, Koji; Mizoguchi, Masahiro; Hata, Nobuhiro; Murata, Hideki; Hatae, Ryusuke; Amano, Toshiyuki; Nakamizo, Akira; Sasaki, Tomio

    2012-01-01

    Many conventional chemotherapeutic drugs exert their cytotoxic function by inducing DNA damage in the tumor cell. Therefore, a cell-inherent DNA repair pathway, which reverses the DNA-damaging effect of the cytotoxic drugs, can mediate therapeutic resistance to chemotherapy. The monofunctional DNA-alkylating agent temozolomide (TMZ) is a commonly used chemotherapeutic drug and the gold standard treatment for glioblastoma (GBM). Although the activity of DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) has been described as the main modulator to determine the sensitivity of GBM to TMZ, a subset of GBM does not respond despite MGMT inactivation, suggesting that another DNA repair mechanism may also modulate the tolerance to TMZ. Considerable interest has focused on MGMT, mismatch repair (MMR), and the base excision repair (BER) pathway in the mechanism of mediating TMZ resistance, but emerging roles for the DNA strand-break repair pathway have been demonstrated. In the first part of this review article, we briefly review the significant role of MGMT, MMR, and the BER pathway in the tolerance to TMZ; in the last part, we review the recent publications that demonstrate possible roles of DNA strand-break repair pathways, such as single-strand break repair and double-strand break repair, as well as the Fanconi anemia pathway in the repair process after alkylating agent-based therapy. It is possible that all of these repair pathways have a potential to modulate the sensitivity to TMZ and aid in overcoming the therapeutic resistance in the clinic.

  4. Complex DNA repair pathways as possible therapeutic targets to overcome temozolomide resistance in glioblastoma

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimoto, Koji; Mizoguchi, Masahiro; Hata, Nobuhiro; Murata, Hideki; Hatae, Ryusuke; Amano, Toshiyuki; Nakamizo, Akira; Sasaki, Tomio, E-mail: kyoshimo@ns.med.kyushu-u.ac.jp [Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka (Japan)

    2012-12-05

    Many conventional chemotherapeutic drugs exert their cytotoxic function by inducing DNA damage in the tumor cell. Therefore, a cell-inherent DNA repair pathway, which reverses the DNA-damaging effect of the cytotoxic drugs, can mediate therapeutic resistance to chemotherapy. The monofunctional DNA-alkylating agent temozolomide (TMZ) is a commonly used chemotherapeutic drug and the gold standard treatment for glioblastoma (GBM). Although the activity of DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) has been described as the main modulator to determine the sensitivity of GBM to TMZ, a subset of GBM does not respond despite MGMT inactivation, suggesting that another DNA repair mechanism may also modulate the tolerance to TMZ. Considerable interest has focused on MGMT, mismatch repair (MMR), and the base excision repair (BER) pathway in the mechanism of mediating TMZ resistance, but emerging roles for the DNA strand-break repair pathway have been demonstrated. In the first part of this review article, we briefly review the significant role of MGMT, MMR, and the BER pathway in the tolerance to TMZ; in the last part, we review the recent publications that demonstrate possible roles of DNA strand-break repair pathways, such as single-strand break repair and double-strand break repair, as well as the Fanconi anemia pathway in the repair process after alkylating agent-based therapy. It is possible that all of these repair pathways have a potential to modulate the sensitivity to TMZ and aid in overcoming the therapeutic resistance in the clinic.

  5. Nucleotide excision repair in the test tube.

    NARCIS (Netherlands)

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

    1995-01-01

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

  6. Optical characteristics of BaGa{sub 2}S{sub 4}:Ho{sup 3+} and BaGa{sub 2}Se{sub 4}:Ho{sup 3+} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Choe, Sung-Hyu [Chosun University, Kwangju (Korea, Republic of); Jin, Moon-Seog [Dongshin University, Naju (Korea, Republic of); Kim, Wha-Tek [Chonnam National University, Kwangju (Korea, Republic of)

    2005-11-15

    BaGa{sub 2}S{sub 4}, BaGa{sub 2}S{sub 4}:Ho{sup 3+}, BaGa{sub 2}Se{sub 4}, and BaGa{sub 2}Se{sub 4}:Ho{sup 3+} single crystals were grown by using the chemical transport reaction method. The optical energy gaps of the single crystals were investigated in the temperature region from 11 K to 300 K. The temperature dependence of the optical energy gap was well fitted by the Varshni equation. Two broad emission bands were observed in the photoluminescence spectra of the single crystals. These bands were attributed to donor-acceptor pair recombinations. Sharp emission peaks were observed in the BaGa{sub 2}S{sub 4}:Ho{sup 3+} and the BaGa{sub 2}Se{sub 4}:Ho{sup 3+} single crystals and were assigned to radiation recombination between split Stark levels of Ho{sup 3+}.

  7. Prediction of peripheral neuropathy in multiple myeloma patients receiving bortezomib and thalidomide: a genetic study based on a single nucleotide polymorphism array.

    Science.gov (United States)

    García-Sanz, Ramón; Corchete, Luis Antonio; Alcoceba, Miguel; Chillon, María Carmen; Jiménez, Cristina; Prieto, Isabel; García-Álvarez, María; Puig, Noemi; Rapado, Immaculada; Barrio, Santiago; Oriol, Albert; Blanchard, María Jesús; de la Rubia, Javier; Martínez, Rafael; Lahuerta, Juan José; González Díaz, Marcos; Mateos, María Victoria; San Miguel, Jesús Fernando; Martínez-López, Joaquín; Sarasquete, María Eugenia

    2017-12-01

    Bortezomib- and thalidomide-based therapies have significantly contributed to improved survival of multiple myeloma (MM) patients. However, treatment-induced peripheral neuropathy (TiPN) is a common adverse event associated with them. Risk factors for TiPN in MM patients include advanced age, prior neuropathy, and other drugs, but there are conflicting results about the role of genetics in predicting the risk of TiPN. Thus, we carried out a genome-wide association study based on more than 300 000 exome single nucleotide polymorphisms in 172 MM patients receiving therapy involving bortezomib and thalidomide. We compared patients developing and not developing TiPN under similar treatment conditions (GEM05MAS65, NCT00443235). The highest-ranking single nucleotide polymorphism was rs45443101, located in the PLCG2 gene, but no significant differences were found after multiple comparison correction (adjusted P = .1708). Prediction analyses, cytoband enrichment, and pathway analyses were also performed, but none yielded any significant findings. A copy number approach was also explored, but this gave no significant results either. In summary, our study did not find a consistent genetic component associated with TiPN under bortezomib and thalidomide therapies that could be used for prediction, which makes clinical judgment essential in the practical management of MM treatment. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Low-leakage superconducting tunnel junctions with a single-crystal Al{sub 2}O{sub 3} barrier

    Energy Technology Data Exchange (ETDEWEB)

    Oh, S [National Institute of Standards and Technology, Boulder, CO 80305 (United States); Department of Physics, University of Illinois, Urbana, IL 61801 (United States); Cicak, K; Osborn, K D; Simmonds, R W; Pappas, D P [National Institute of Standards and Technology, Boulder, CO 80305 (United States); McDermott, R; Cooper, K B; Steffen, M; Martinis, J M [University of California, Santa Barbara, CA 93106 (United States)

    2005-10-01

    We have developed a two-step growth scheme for single-crystal Al{sub 2}O{sub 3} tunnel barriers. The barriers are epitaxially grown on single-crystal rhenium (Re) base electrodes that are grown epitaxially on a sapphire substrate, while polycrystalline Al is used as the top electrode. We show that by first growing an amorphous aluminium (Al) oxide layer at room temperature and crystallizing it at a high temperature in oxygen environment, a morphologically intact single-crystal Al{sub 2}O{sub 3} layer is obtained. Tunnel junctions fabricated from these trilayers show very low subgap leakage current. This single-crystal Al{sub 2}O{sub 3} junction may open a new venue for coherent quantum devices.

  9. Typing of canine parvovirus isolates using mini-sequencing based single nucleotide polymorphism analysis.

    Science.gov (United States)

    Naidu, Hariprasad; Subramanian, B Mohana; Chinchkar, Shankar Ramchandra; Sriraman, Rajan; Rana, Samir Kumar; Srinivasan, V A

    2012-05-01

    The antigenic types of canine parvovirus (CPV) are defined based on differences in the amino acids of the major capsid protein VP2. Type specificity is conferred by a limited number of amino acid changes and in particular by few nucleotide substitutions. PCR based methods are not particularly suitable for typing circulating variants which differ in a few specific nucleotide substitutions. Assays for determining SNPs can detect efficiently nucleotide substitutions and can thus be adapted to identify CPV types. In the present study, CPV typing was performed by single nucleotide extension using the mini-sequencing technique. A mini-sequencing signature was established for all the four CPV types (CPV2, 2a, 2b and 2c) and feline panleukopenia virus. The CPV typing using the mini-sequencing reaction was performed for 13 CPV field isolates and the two vaccine strains available in our repository. All the isolates had been typed earlier by full-length sequencing of the VP2 gene. The typing results obtained from mini-sequencing matched completely with that of sequencing. Typing could be achieved with less than 100 copies of standard plasmid DNA constructs or ≤10¹ FAID₅₀ of virus by mini-sequencing technique. The technique was also efficient for detecting multiple types in mixed infections. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. BER estimation for all-optical regenerators influenced by pattern effects

    DEFF Research Database (Denmark)

    Bischoff, Svend; Lading, B.; Mørk, Jesper

    2002-01-01

    An efficient method is presented for the estimation of the bit-error rate (BER) of a system employing all-optical regenerators influenced by pattern effects. We theoretically study noise accumulation and noise redistribution in long distance transmission systems employing a delayed interference...... signal wavelength converter for all-optical regeneration. The BER is studied for return-to-zero signals at bit rates of 2.5 Gb/s (no patterning) up to 40 Gb/s (strong patterning). The calculation of the BER is based on pattern dependent transfer functions, which may be obtained numerically or measured....

  11. Allelic variation of the Waxy gene in foxtail millet [Setaria italica (L.) P. Beauv.] by single nucleotide polymorphisms.

    Science.gov (United States)

    Van, K; Onoda, S; Kim, M Y; Kim, K D; Lee, S-H

    2008-03-01

    The Waxy (Wx) gene product controls the formation of a straight chain polymer of amylose in the starch pathway. Dominance/recessiveness of the Wx allele is associated with amylose content, leading to non-waxy/waxy phenotypes. For a total of 113 foxtail millet accessions, agronomic traits and the molecular differences of the Wx gene were surveyed to evaluate genetic diversities. Molecular types were associated with phenotypes determined by four specific primer sets (non-waxy, Type I; low amylose, Type VI; waxy, Type IV or V). Additionally, the insertion of transposable element in waxy was confirmed by ex1/TSI2R, TSI2F/ex2, ex2int2/TSI7R and TSI7F/ex4r. Seventeen single nucleotide polymorphims (SNPs) were observed from non-coding regions, while three SNPs from coding regions were non-synonymous. Interestingly, the phenotype of No. 88 was still non-waxy, although seven nucleotides (AATTGGT) insertion at 2,993 bp led to 78 amino acids shorter. The rapid decline of r (2) in the sequenced region (exon 1-intron 1-exon 2) suggested a low level of linkage disequilibrium and limited haplotype structure. K (s) values and estimation of evolutionary events indicate early divergence of S. italica among cereal crops. This study suggested the Wx gene was one of the targets in the selection process during domestication.

  12. Genome-wide map of Apn1 binding sites under oxidative stress in Saccharomyces cerevisiae.

    Science.gov (United States)

    Morris, Lydia P; Conley, Andrew B; Degtyareva, Natalya; Jordan, I King; Doetsch, Paul W

    2017-11-01

    The DNA is cells is continuously exposed to reactive oxygen species resulting in toxic and mutagenic DNA damage. Although the repair of oxidative DNA damage occurs primarily through the base excision repair (BER) pathway, the nucleotide excision repair (NER) pathway processes some of the same lesions. In addition, damage tolerance mechanisms, such as recombination and translesion synthesis, enable cells to tolerate oxidative DNA damage, especially when BER and NER capacities are exceeded. Thus, disruption of BER alone or disruption of BER and NER in Saccharomyces cerevisiae leads to increased mutations as well as large-scale genomic rearrangements. Previous studies demonstrated that a particular region of chromosome II is susceptible to chronic oxidative stress-induced chromosomal rearrangements, suggesting the existence of DNA damage and/or DNA repair hotspots. Here we investigated the relationship between oxidative damage and genomic instability utilizing chromatin immunoprecipitation combined with DNA microarray technology to profile DNA repair sites along yeast chromosomes under different oxidative stress conditions. We targeted the major yeast AP endonuclease Apn1 as a representative BER protein. Our results indicate that Apn1 target sequences are enriched for cytosine and guanine nucleotides. We predict that BER protects these sites in the genome because guanines and cytosines are thought to be especially susceptible to oxidative attack, thereby preventing large-scale genome destabilization from chronic accumulation of DNA damage. Information from our studies should provide insight into how regional deployment of oxidative DNA damage management systems along chromosomes protects against large-scale rearrangements. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  13. Distinctive features of single nucleotide alterations in induced pluripotent stem cells with different types of DNA repair deficiency disorders

    Science.gov (United States)

    Okamura, Kohji; Sakaguchi, Hironari; Sakamoto-Abutani, Rie; Nakanishi, Mahito; Nishimura, Ken; Yamazaki-Inoue, Mayu; Ohtaka, Manami; Periasamy, Vaiyapuri Subbarayan; Alshatwi, Ali Abdullah; Higuchi, Akon; Hanaoka, Kazunori; Nakabayashi, Kazuhiko; Takada, Shuji; Hata, Kenichiro; Toyoda, Masashi; Umezawa, Akihiro

    2016-01-01

    Disease-specific induced pluripotent stem cells (iPSCs) have been used as a model to analyze pathogenesis of disease. In this study, we generated iPSCs derived from a fibroblastic cell line of xeroderma pigmentosum (XP) group A (XPA-iPSCs), a rare autosomal recessive hereditary disease in which patients develop skin cancer in the areas of skin exposed to sunlight. XPA-iPSCs exhibited hypersensitivity to ultraviolet exposure and accumulation of single-nucleotide substitutions when compared with ataxia telangiectasia-derived iPSCs that were established in a previous study. However, XPA-iPSCs did not show any chromosomal instability in vitro, i.e. intact chromosomes were maintained. The results were mutually compensating for examining two major sources of mutations, nucleotide excision repair deficiency and double-strand break repair deficiency. Like XP patients, XPA-iPSCs accumulated single-nucleotide substitutions that are associated with malignant melanoma, a manifestation of XP. These results indicate that XPA-iPSCs may serve a monitoring tool (analogous to the Ames test but using mammalian cells) to measure single-nucleotide alterations, and may be a good model to clarify pathogenesis of XP. In addition, XPA-iPSCs may allow us to facilitate development of drugs that delay genetic alteration and decrease hypersensitivity to ultraviolet for therapeutic applications. PMID:27197874

  14. Preparation of chitin–silica composites by in vitro silicification of two-dimensional Ianthella basta demosponge chitinous scaffolds under modified Stöber conditions

    Energy Technology Data Exchange (ETDEWEB)

    Wysokowski, Marcin [Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, M. Skłodowskiej-Curie 2, PL-60965 Poznan (Poland); Behm, Thomas [Institute of Experimental Physics, TU Bergakademie Freiberg, Liepziger 23, 09599 Freiberg (Germany); Born, René [Institute of Materials Science, Dresden University of Technology, Helmholtzstraße 10, 01069 Dresden (Germany); Bazhenov, Vasilii V. [Institute of Experimental Physics, TU Bergakademie Freiberg, Liepziger 23, 09599 Freiberg (Germany); Meißner, Heike; Richter, Gert [Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Fetscherstraße 74, 01307 Dresden (Germany); Szwarc-Rzepka, Karolina [Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, M. Skłodowskiej-Curie 2, PL-60965 Poznan (Poland); Makarova, Anna; Vyalikh, Denis [Institute of Solid State Physics, Dresden University of Technology, Helmholtzstraße 10, 01069 Dresden (Germany); Schupp, Peter [Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Emsstr. 20, 26382 Wilhelmshaven (Germany); Jesionowski, Teofil, E-mail: teofil.jesionowski@put.poznan.pl [Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, M. Skłodowskiej-Curie 2, PL-60965 Poznan (Poland); Ehrlich, Hermann, E-mail: hermann.ehrlich@physik.tu-freiberg.de [Institute of Experimental Physics, TU Bergakademie Freiberg, Liepziger 23, 09599 Freiberg (Germany)

    2013-10-15

    Chitin is a biopolymer found in cell walls of various fungi and skeletal structures of numerous invertebrates. The occurrence of chitin within calcium- and silica-containing biominerals has inspired development of chitin-based hybrids and composites in vitro with specific physico-chemical and material properties. We show here for the first time that the two-dimensional α-chitin scaffolds isolated from the skeletons of marine demosponge Ianthella basta can be effectively silicified by the two-step method with the use of Stöber silica micro- and nanodispersions under Extreme Biomimetic conditions. The chitin–silica composites obtained at 120 °C were characterized by the presence of spherical SiO{sub 2} particles homogeneously distributed over the chitin fibers, which probably follows from the compatibility of Si–OH groups to the hydroxyl groups of chitin. The biocomposites obtained were characterized by various analytical techniques such as energy dispersive spectrometry, scanning electron microscopy, thermogravimetric/differential thermal analyses as well as X-ray photoelectron spectroscopy, Fourier transform infrared and Raman spectroscopy to determine possible interactions between silica and chitin molecule. The results presented proved that the character and course of the in vitro chitin silicification in Stöber dispersions depended considerably on the degree of hydrolysis of the SiO{sub 2} precursor. - Highlights: • 2D α-chitin scaffolds isolated from marine demosponge can be effectively silicified using Stöber silica. • The chitin–silica composites were obtained under Extreme Biomimetic conditions. • Character and course of the in vitro chitin silicification in Stöber dispersions is discussed.

  15. Growth and Characterization of Ce- Substituted Nd<sub>2sub>Fe>14sub>11B Single Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Susner, M. A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Materials Science and Technology Division; Conner, B. S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Materials Science and Technology Division; Saparov, B. I. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Materials Science and Technology Division; McGuire, M. A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Materials Science and Technology Division; Crumlin, E. J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source; Veith, G. M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source; Cao, H. B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Quantum Condensed Matter Division; Shanavas, K. V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Materials Science and Technology Division; Parker, D. S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Materials Science and Technology Division; Chakoumakos, B. C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Quantum Condensed Matter Division; Sales, B. C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Materials Science and Technology Division

    2015-08-31

    Single crystals of (Nd<sub>1-xsub>Cex)>2sub>Fe>14sub>B are grown out of Fe-(Nd,Ce) flux. Chemical and structural analysis of the crystals indicates that (Nd<sub>1-xsub>Cex)>2sub>Fe>14sub>B forms a solid solution until at least x = 0.38 with a Vegard-like variation of the lattice constants with x. Refinements of single crystal neutron diffraction data indicate that Ce has a slight site preference (7:3) for the 4g rare earth site over the 4f site. Furthermore, magnetization measurements show that for x = 0.38 the saturation magnetization at 400 K, a temperature important to applications, falls from 29.8 for the parent Nd<sub>2sub>Fe>14sub>B to 27.6 μ<sub>B>/f.u., the anisotropy field decreases from 5.5 T to 4.7 T, and the Curie temperature decreases from 586 to 543 K. First principles calculations carried out within density functional theory are used to explain the decrease in magnetic properties due to Ce substitution. Although the presence of the lower-cost and more abundant Ce slightly affects these important magnetic characteristics, this decrease is not large enough to affect a multitude of applications. Ce-substituted Nd<sub>2sub>Fe>14sub>B is therefore a potential high-performance permanent magnet material with substantially reduced Nd content.

  16. Synthesis, microstructure and magnetic properties of Fe{sub 3}Si{sub 0.7}Al{sub 0.3}@SiO{sub 2} core–shell particles and Fe{sub 3}Si/Al{sub 2}O{sub 3} soft magnetic composite core

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jian, E-mail: snove418562@163.com [The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Fan, Xi’an, E-mail: groupfxa@163.com [The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Wu, Zhaoyang, E-mail: wustwuzhaoyang@163.com [The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Li, Guangqiang [The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China)

    2015-11-15

    Fe{sub 3}Si{sub 0.7}Al{sub 0.3}@SiO{sub 2} core–shell particles and Fe{sub 3}Si/Al{sub 2}O{sub 3} soft magnetic composite core have been synthesized via a modified stöber method combined with following high temperature sintering process. Most of conductive Fe{sub 3}Si{sub 0.7}Al{sub 0.3} particles could be uniformly coated by insulating SiO{sub 2} using the modified stöber method. The Fe{sub 3}Si{sub 0.7}Al{sub 0.3}@SiO{sub 2} core–shell particles exhibited good soft magnetic properties with low coercivity and high saturation magnetization. The reaction 4Al+3SiO{sub 2}=2α-Al{sub 2}O{sub 3}+3Si took place during the sintering process. As a result the new Fe{sub 3}Si/Al{sub 2}O{sub 3} composite was formed. The Fe{sub 3}Si/Al{sub 2}O{sub 3} composite core displayed more excellent soft magnetic properties, better frequency stability at high frequencies, much higher electrical resistivity and lower core loss than the pure Fe{sub 3}Si{sub 0.7}Al{sub 0.3} core. The method of introducing insulating layers surrounding magnetic particles provides a promising route to develop new and high compact soft magnetic materials with good magnetic and electric properties. - Graphical abstract: In Fe{sub 3}Si/Al{sub 2}O{sub 3} composite, Fe{sub 3}Si phases are separated by Al{sub 2}O{sub 3} layers and the eddy currents are confined in Fe{sub 3}Si phases, thus increasing resistivity and reducing core loss. - Highlights: • Fe{sub 3}Si{sub 0.7}Al{sub 0.3}@SiO{sub 2} core–shell particles and Fe{sub 3}Si/Al{sub 2}O{sub 3} cores were prepared. • Fe{sub 3}Si{sub 0.7}Al{sub 0.3} particles could be uniformly coated by nano-sized SiO{sub 2} clusters. • Fe{sub 3}Si{sub 0.7}Al{sub 0.3}@SiO{sub 2} particles and Fe{sub 3}Si/Al{sub 2}O{sub 3} cores showed good soft magnetic properties. • Fe{sub 3}Si/Al{sub 2}O{sub 3} had lower core loss and better frequency stability than Fe{sub 3}Si{sub 0.7}Al{sub 0.3} cores.

  17. {sup 57}Fe Mössbauer spectroscopic studies of single-crystalline K{sub x}Fe{sub 2-y}S{sub 2} and K{sub x}Fe{sub 2-y}Se{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, Yuu, E-mail: tsuchiya.yuu1990@gmail.com; Ikeda, Shugo; Kobayashi, Hisao [University of Hyogo (Japan)

    2016-12-15

    We have investigated the physical properties of single-crystalline K{sub x}Fe{sub 2-y}S{sub 2} and K{sub x}Fe{sub 2-y}Se{sub 2} samples using {sup 57}Fe Mössbauer spectroscopy. The observed {sup 57}Fe Mössbauer spectra were reconstructed using a major antiferromagnetic ordered K{sub 2}Fe{sub 4}Se{sub 5} phase and a minor paramagnetic phase down to 5 K, despite being superconducting below 32.2 K in K{sub x}Fe{sub 2-y}Se{sub 2}. The analysis of {sup 57}Fe Mössbauer spectrum for K{sub x}Fe{sub 2-y}S{sub 2} at 290 K confirms the presence of a major antiferromagnetic ordered K{sub 2}Fe{sub 4}S{sub 5} phase and a minor paramagnetic phase in the K{sub x}Fe{sub 2-y}S{sub 2} single crystal. The derived hyperfine interaction parameters of the paramagnetic phase in K{sub x}Fe{sub 2-y}S{sub 2} suggest that the microstructure of this phase in K{sub x}Fe{sub 2-y}S{sub 2} is similar to that of the superconducting phase in K{sub x}Fe{sub 2-y}Se{sub 2} although the K{sub x}Fe{sub 2-y}S{sub 2} single crystals exhibit no superconductivity down to 5 K.

  18. DNA repair in neurons: So if they don't divide what's to repair?

    International Nuclear Information System (INIS)

    Fishel, Melissa L.; Vasko, Michael R.; Kelley, Mark R.

    2007-01-01

    Neuronal DNA repair remains one of the most exciting areas for investigation, particularly as a means to compare the DNA repair response in mitotic (cancer) vs. post-mitotic (neuronal) cells. In addition, the role of DNA repair in neuronal cell survival and response to aging and environmental insults is of particular interest. DNA damage caused by reactive oxygen species (ROS) such as generated by mitochondrial respiration includes altered bases, abasic sites, and single- and double-strand breaks which can be prevented by the DNA base excision repair (BER) pathway. Oxidative stress accumulates in the DNA of the human brain over time especially in the mitochondrial DNA (mtDNA) and is proposed to play a critical role in aging and in the pathogenesis of several neurological disorders including Parkinson's disease, ALS, and Alzheimer's diseases. Because DNA damage accumulates in the mtDNA more than nuclear DNA, there is increased interest in DNA repair pathways and the consequence of DNA damage in the mitochondria of neurons. The type of damage that is most likely to occur in neuronal cells is oxidative DNA damage which is primarily removed by the BER pathway. Following the notion that the bulk of neuronal DNA damage is acquired by oxidative DNA damage and ROS, the BER pathway is a likely area of focus for neuronal studies of DNA repair. BER variations in brain aging and pathology in various brain regions and tissues are presented. Therefore, the BER pathway is discussed in greater detail in this review than other repair pathways. Other repair pathways including direct reversal, nucleotide excision repair (NER), mismatch repair (MMR), homologous recombination and non-homologous end joining are also discussed. Finally, there is a growing interest in the role that DNA repair pathways play in the clinical arena as they relate to the neurotoxicity and neuropathy associated with cancer treatments. Among the numerous side effects of cancer treatments, major clinical effects

  19. DNA repair in neurons: So if they don't divide what's to repair?

    Energy Technology Data Exchange (ETDEWEB)

    Fishel, Melissa L. [Department of Pediatrics (Section of Hematology/Oncology), Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 W. Walnut, Room 302C, Indianapolis, IN 46202 (United States); Vasko, Michael R. [Department of Pharmacology and Toxicology, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN 46202 (United States); Kelley, Mark R. [Department of Pediatrics (Section of Hematology/Oncology), Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 W. Walnut, Room 302C, Indianapolis, IN 46202 (United States) and Department of Pharmacology and Toxicology, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN 46202 (United States) and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 1044 W. Walnut, Room 302C, Indianapolis, IN 46202 (United States)]. E-mail: mkelley@iupui.edu

    2007-01-03

    Neuronal DNA repair remains one of the most exciting areas for investigation, particularly as a means to compare the DNA repair response in mitotic (cancer) vs. post-mitotic (neuronal) cells. In addition, the role of DNA repair in neuronal cell survival and response to aging and environmental insults is of particular interest. DNA damage caused by reactive oxygen species (ROS) such as generated by mitochondrial respiration includes altered bases, abasic sites, and single- and double-strand breaks which can be prevented by the DNA base excision repair (BER) pathway. Oxidative stress accumulates in the DNA of the human brain over time especially in the mitochondrial DNA (mtDNA) and is proposed to play a critical role in aging and in the pathogenesis of several neurological disorders including Parkinson's disease, ALS, and Alzheimer's diseases. Because DNA damage accumulates in the mtDNA more than nuclear DNA, there is increased interest in DNA repair pathways and the consequence of DNA damage in the mitochondria of neurons. The type of damage that is most likely to occur in neuronal cells is oxidative DNA damage which is primarily removed by the BER pathway. Following the notion that the bulk of neuronal DNA damage is acquired by oxidative DNA damage and ROS, the BER pathway is a likely area of focus for neuronal studies of DNA repair. BER variations in brain aging and pathology in various brain regions and tissues are presented. Therefore, the BER pathway is discussed in greater detail in this review than other repair pathways. Other repair pathways including direct reversal, nucleotide excision repair (NER), mismatch repair (MMR), homologous recombination and non-homologous end joining are also discussed. Finally, there is a growing interest in the role that DNA repair pathways play in the clinical arena as they relate to the neurotoxicity and neuropathy associated with cancer treatments. Among the numerous side effects of cancer treatments, major

  20. LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E

    DEFF Research Database (Denmark)

    Jacobsen, Nana; Bentzen, Joan; Meldgaard, Michael

    2002-01-01

    Genotyping of single nucleotide polymorphisms (SNPs) in large populations presents a great challenge, especially if the SNPs are embedded in GC-rich regions, such as the codon 112 SNP in the human apolipoprotein E (apoE). In the present study, we have used immobilized locked nucleic acid (LNA...... was applied to a panel of patient samples with simultaneous genotyping of the patients by DNA sequencing. The apoE genotyping assays for the codons 112 and 158 SNPs resulted in unambiguous results for all patient samples, concurring with those obtained by DNA sequencing....

  1. Development and characterization of 35 single nucleotide polymorphism markers for the brown alga Fucus vesiculosus

    NARCIS (Netherlands)

    Canovas, Fernando; Mota, Catarina; Ferreira-Costa, Joana; Serrao, Ester; Coyer, Jim; Olsen, Jeanine; Pearson, Gareth

    2011-01-01

    We characterized 35 single nucleotide polymorphism (SNP) markers for the brown alga Fucus vesiculosus. Based on existing Fucus Expressed Sequence Tag libraries for heat and desiccation-stressed tissue, SNPs were developed and confirmed by re-sequencing cDNA from a diverse panel of individuals. SNP

  2. Synthesis and reactivity of single-phase Be{sub 17}Ti{sub 2} intermetallic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jae-Hwan, E-mail: kim.jaehwan@jaea.go.jp [Breeding Functional Materials Development Group, Sector of Fusion Research and Development, Japan Atomic Energy Agency (Japan); Iwakiri, Hirotomo; Furugen, Tatsuaki [Faculty of Education Elementary and Secondary School Teacher Training Program, University of the Ryukyus, Okinawa (Japan); Nakamichi, Masaru [Breeding Functional Materials Development Group, Sector of Fusion Research and Development, Japan Atomic Energy Agency (Japan)

    2016-01-15

    Highlights: • Preliminary synthesis of single-phase Be{sub 17}Ti{sub 2} was succeeded. • Reactivity difference between beryllium and beryllides may be caused by a lattice strain. • Oxidation of Be{sub 17}Ti{sub 2} at high temperatures results in the formation of TiO{sub 2}. • Simulation results reveal that a stable site for hydrogen at the center of tetrahedron exists. - Abstract: To investigate feasibility for application of Be{sub 17}Ti{sub 2} as a neutron multiplier as well as a refractory material, single-phase Be{sub 17}Ti{sub 2} intermetallic compounds were synthesized using an annealing heat treatment of the starting powder and a plasma sintering method. Scanning electron microscopic observations and X-ray diffraction measurements reveal that the single-phase Be{sub 17}Ti{sub 2} compounds were successfully synthesized. We examined the reactivity of Be{sub 17}Ti{sub 2} with 1% H{sub 2}O and discovered that a larger stoichiometric amount of Ti resulted in the formation of TiO{sub 2} on the surface at high temperatures. This oxidation may also contribute to an increase in both weight gain and generation of H{sub 2}. This suggests that the formation of the Ti-depleted Be{sub 17}Ti{sub 2−x} layer as a result of oxidation facilitates an increased reactivity with H{sub 2}O. To evaluate the safety aspects of Be{sub 17}Ti{sub 2}, we also investigated the hydrogen positions and solution energies based on the first principle. The calculations reveal that there are 10 theoretical sites, where 9 of these sites have hydrogen solution energies with a positive value (endothermic) and 1 site located at the center of a tetrahedron comprising two Be and two Ti atoms gives a negative value (exothermic).

  3. Single Nucleotide Polymorphism Analysis of Protamine Genes in Infertile Men

    Directory of Open Access Journals (Sweden)

    Ahamad Salamian

    2008-01-01

    Full Text Available Background: Single nucleotide polymorphism (SNPs are considered as one of the underlyingcauses of male infertility. Proper sperm chromatin packaging which involves replacement ofhistones with protamines has profound effect on male fertility. Over 20 SNPs have been reportedfor the protamine 1 and 2.Materials and Methods: The aim of this study was to evaluate the frequency of two previouslyreported SNPs using polymerase chain reaction (PCR-restriction fragment length polymorphism(RFLP approach in 35, 96 and 177 normal, oligozoospermic and azoospermic individuals. TheseSNPs are: 1. A base pair substitution (G at position 197 instead of T in protamine type 1 Openreading frame (ORF including untranslated region, which causes an Arg residue change to Serresidue in a highly conserved region. 2. cytidine nucleotide change to thymidine in position of 248of protamine type 2 ORF which caused a nonsense point mutation.Results: The two mentioned SNPs were not present in the studied population, thus concluding thatthese SNPs can not serves as molecular markers for male infertility diagnosis.Conclusion: The results of our study reveal that in a selected Iranian population, the SNP G197Tand C248T are completely absent and are not associated with male infertility and therefore theseSNPs may not represent a molecular marker for genetic diagnosis of male infertility.

  4. Preparation and oxidation resistance of single crystalline β-Zn{sub 4}Sb{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hong-xia; Deng, Shu-ping [Education Ministry Key Laboratory of Renewable Energy Advanced Materials and Manufacturing Technology, Yunnan Normal University, Kunming 650500 (China); Li, De-cong [Photoelectric Engineering College, Yunnan Open University, Kunming 650500 (China); Shen, Lan-xian; Cheng, Feng; Wang, Jin-song [Education Ministry Key Laboratory of Renewable Energy Advanced Materials and Manufacturing Technology, Yunnan Normal University, Kunming 650500 (China); Deng, Shu-kang, E-mail: skdeng@126.com [Education Ministry Key Laboratory of Renewable Energy Advanced Materials and Manufacturing Technology, Yunnan Normal University, Kunming 650500 (China)

    2016-11-01

    This study prepared a Zn-rich single crystal β-Zn{sub 4}Sb{sub 3} using a Sn flux method based on the stoichiometric ratios of Zn{sub 4.4}Sb{sub 3}Sn{sub 3}. The oxidation resistance of the sample was determined by exploring the effects of heat treatment in air on electrical transport properties and thermal stability, which is of practical importance in the application of the material at high temperatures. Results showed that the prepared sample possessed high electrical transport properties, with a high power factor of 1.67×10{sup −3} W m{sup −1} K{sup −2} at 563 K. The heat treatment in air weakened the electrical conductivity of the single crystalline β-Zn{sub 4}Sb{sub 3}, whereas the Seebeck coefficients were rarely independent of the annealing condition. Eventually, the power factor obtained after the first heating at 523 K for 4 h became comparable to that of the as-prepared sample, although it decreased after the second heating at 573 K for 5 h. Nevertheless, the single crystalline β-Zn{sub 4}Sb{sub 3} still possessed a good thermal stability after the heat treatment process.

  5. Precise detection of de novo single nucleotide variants in human genomes.

    Science.gov (United States)

    Gómez-Romero, Laura; Palacios-Flores, Kim; Reyes, José; García, Delfino; Boege, Margareta; Dávila, Guillermo; Flores, Margarita; Schatz, Michael C; Palacios, Rafael

    2018-05-07

    The precise determination of de novo genetic variants has enormous implications across different fields of biology and medicine, particularly personalized medicine. Currently, de novo variations are identified by mapping sample reads from a parent-offspring trio to a reference genome, allowing for a certain degree of differences. While widely used, this approach often introduces false-positive (FP) results due to misaligned reads and mischaracterized sequencing errors. In a previous study, we developed an alternative approach to accurately identify single nucleotide variants (SNVs) using only perfect matches. However, this approach could be applied only to haploid regions of the genome and was computationally intensive. In this study, we present a unique approach, coverage-based single nucleotide variant identification (COBASI), which allows the exploration of the entire genome using second-generation short sequence reads without extensive computing requirements. COBASI identifies SNVs using changes in coverage of exactly matching unique substrings, and is particularly suited for pinpointing de novo SNVs. Unlike other approaches that require population frequencies across hundreds of samples to filter out any methodological biases, COBASI can be applied to detect de novo SNVs within isolated families. We demonstrate this capability through extensive simulation studies and by studying a parent-offspring trio we sequenced using short reads. Experimental validation of all 58 candidate de novo SNVs and a selection of non-de novo SNVs found in the trio confirmed zero FP calls. COBASI is available as open source at https://github.com/Laura-Gomez/COBASI for any researcher to use. Copyright © 2018 the Author(s). Published by PNAS.

  6. Spin coherence in a Mn{sub 3} single-molecule magnet

    Energy Technology Data Exchange (ETDEWEB)

    Abeywardana, Chathuranga [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Mowson, Andrew M.; Christou, George [Department of Chemistry, University of Florida, Gainesville, Florida 32611 (United States); Takahashi, Susumu, E-mail: susumu.takahashi@usc.edu [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Department of Physics, University of Southern California, Los Angeles, California 90089 (United States)

    2016-01-25

    Spin coherence in single crystals of the spin S = 6 single-molecule magnet (SMM) [Mn{sub 3}O(O{sub 2}CEt){sub 3}(mpko){sub 3}]{sup +} (abbreviated Mn{sub 3}) has been investigated using 230 GHz electron paramagnetic resonance spectroscopy. Coherence in Mn{sub 3} was uncovered by significantly suppressing dipolar contribution to the decoherence with complete spin polarization of Mn{sub 3} SMMs. The temperature dependence of spin decoherence time (T{sub 2}) revealed that the dipolar decoherence is the dominant source of decoherence in Mn{sub 3} and T{sub 2} can be extended up to 267 ns by quenching the dipolar decoherence.

  7. Bemerkungen über Pedipalpi (Fortsetzung)

    NARCIS (Netherlands)

    Speijer, E.A.M.

    1931-01-01

    In meiner vorigen Mitteilung (Bemerkungen über Pedipalpi, Zoologische Mededeelingen 's Rijks Museum van Natuurlijke Historie te Leiden Deel XIV, Afl. 1—2, 1931, p. 79—88) habe ich schon darauf hingewiesen, dass man bei der Bearbeitung der Thelyphonidae auf eigentümliche Schwierigkeiten stösst. Diese

  8. Morphology and kinetics of polymorphic transformations in K{sub 0.965}Rb{sub 0.035}NO{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Nasirov, V. I.; Bairamov, R. B., E-mail: bayramov.razim@mail.ru; Nasirov, E. V. [Academy of Sciences of Azerbaijan, Institute of Physics (Azerbaijan)

    2015-12-15

    Polymorphic transformations in K{sub 0.965}Rb{sub 0.035}NO{sub 3} single crystals have been investigated by optical microscopy and X-ray diffraction. The equilibrium temperature between modifications II and III of the crystal studied is determined to be T = 452 ± 0.5 K. It is found that polymorphic transformations are of the single crystal ↔ single crystal type and occur with the formation and growth of nuclei of new crystals in matrix ones at II ↔ III transformations. An empirical dependence of the growth rate of modification III on temperature is established in the form ϑ = ϑ = (–0.478ΔT + 0.712ΔT{sup 2}–0.00041ΔT{sup 3}) × 10{sup –2} cm/s (ΔT = T{sub tr}–T{sub 0}, where T{sub tr} is the transformation temperature and T{sub 0} is the equilibrium temperature)

  9. Analysis of the intronic single nucleotide polymorphism rs#466452 of the nephrin gene in patients with diabetic nephropathy

    Directory of Open Access Journals (Sweden)

    RODRIGO GONZÁLEZ

    2009-01-01

    Full Text Available We present the analysis of an intronic polymorphism of the nephrin gene and its relationship to the development of diabetic nephropathy in a study of diabetes type 1 and type 2 patients. The frequency of the single nucleotide polymorphism rs#466452 in the nephrin gene was determined in 231 patients and control subjects. The C/T status of the polymorphism was assessed using restriction enzyme digestions and the nephrin transcript from a kidney biopsy was examined. Association between the polymorphism and clinical parameters was evaluated using multivaríate correspondence analysis. A bioinformatics analysis of the single nucleotide polymorphism rs#466452 suggested the appearance of a splicing enhancer sequence in intron 24 of the nephrin gene and a modification of proteins that bind to this sequence. However, no change in the splicing of a nephrin transcript from a renal biopsy was found. No association was found between the polymorphism and diabetes or degree of renal damage in diabetes type 1 or 2 patients. The single nucleotide polymorphism rs#466452 of the nephrin gene seems to be neutral in relation to diabetes and the development of diabetic nephropathy, and does not affect the splicing of a nephrin transcript, in spite of a splicing enhancer site.

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

    Directory of Open Access Journals (Sweden)

    Ana Osorio

    2014-04-01

    Full Text Available Single Nucleotide Polymorphisms (SNPs in genes involved in the DNA Base Excision Repair (BER pathway could be associated with cancer risk in carriers of mutations in the high-penetrance susceptibility genes BRCA1 and BRCA2, given the relation of synthetic lethality that exists between one of the components of the BER pathway, PARP1 (poly ADP ribose polymerase, and both BRCA1 and BRCA2. In the present study, we have performed a comprehensive analysis of 18 genes involved in BER using a tagging SNP approach in a large series of BRCA1 and BRCA2 mutation carriers. 144 SNPs were analyzed in a two stage study involving 23,463 carriers from the CIMBA consortium (the Consortium of Investigators of Modifiers of BRCA1 and BRCA2. Eleven SNPs showed evidence of association with breast and/or ovarian cancer at p<0.05 in the combined analysis. Four of the five genes for which strongest evidence of association was observed were DNA glycosylases. The strongest evidence was for rs1466785 in the NEIL2 (endonuclease VIII-like 2 gene (HR: 1.09, 95% CI (1.03-1.16, p = 2.7 × 10(-3 for association with breast cancer risk in BRCA2 mutation carriers, and rs2304277 in the OGG1 (8-guanine DNA glycosylase gene, with ovarian cancer risk in BRCA1 mutation carriers (HR: 1.12 95%CI: 1.03-1.21, p = 4.8 × 10(-3. DNA glycosylases involved in the first steps of the BER pathway may be associated with cancer risk in BRCA1/2 mutation carriers and should be more comprehensively studied.

  11. Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA

    OpenAIRE

    Khodakov, Dmitriy A.; Khodakova, Anastasia S.; Huang, David M.; Linacre, Adrian; Ellis, Amanda V.

    2015-01-01

    Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within doubl...

  12. Incorporation of causative quantitative trait nucleotides in single-step GBLUP.

    Science.gov (United States)

    Fragomeni, Breno O; Lourenco, Daniela A L; Masuda, Yutaka; Legarra, Andres; Misztal, Ignacy

    2017-07-26

    Much effort is put into identifying causative quantitative trait nucleotides (QTN) in animal breeding, empowered by the availability of dense single nucleotide polymorphism (SNP) information. Genomic selection using traditional SNP information is easily implemented for any number of genotyped individuals using single-step genomic best linear unbiased predictor (ssGBLUP) with the algorithm for proven and young (APY). Our aim was to investigate whether ssGBLUP is useful for genomic prediction when some or all QTN are known. Simulations included 180,000 animals across 11 generations. Phenotypes were available for all animals in generations 6 to 10. Genotypes for 60,000 SNPs across 10 chromosomes were available for 29,000 individuals. The genetic variance was fully accounted for by 100 or 1000 biallelic QTN. Raw genomic relationship matrices (GRM) were computed from (a) unweighted SNPs, (b) unweighted SNPs and causative QTN, (c) SNPs and causative QTN weighted with results obtained with genome-wide association studies, (d) unweighted SNPs and causative QTN with simulated weights, (e) only unweighted causative QTN, (f-h) as in (b-d) but using only the top 10% causative QTN, and (i) using only causative QTN with simulated weight. Predictions were computed by pedigree-based BLUP (PBLUP) and ssGBLUP. Raw GRM were blended with 1 or 5% of the numerator relationship matrix, or 1% of the identity matrix. Inverses of GRM were obtained directly or with APY. Accuracy of breeding values for 5000 genotyped animals in the last generation with PBLUP was 0.32, and for ssGBLUP it increased to 0.49 with an unweighted GRM, 0.53 after adding unweighted QTN, 0.63 when QTN weights were estimated, and 0.89 when QTN weights were based on true effects known from the simulation. When the GRM was constructed from causative QTN only, accuracy was 0.95 and 0.99 with blending at 5 and 1%, respectively. Accuracies simulating 1000 QTN were generally lower, with a similar trend. Accuracies using the

  13. Core–shell structured FeSiAl/SiO{sub 2} particles and Fe{sub 3}Si/Al{sub 2}O{sub 3} soft magnetic composite cores with tunable insulating layer thicknesses

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Xi’an, E-mail: groupfxa@163.com [The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Wang, Jian, E-mail: snove418562@163.com [The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Wu, Zhaoyang, E-mail: wustwuzhaoyang@163.com [The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Li, Guangqiang, E-mail: ligq-wust@mail.wust.edu.cn [The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China); Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan, Hubei 430081 (China)

    2015-11-15

    Graphical abstract: - Highlights: • FeSiAl/SiO{sub 2} core–shell particles and Fe{sub 3}Si/Al{sub 2}O{sub 3} composite cores were prepared. • SiO{sub 2} surrounding FeSiAl were replaced by Al{sub 2}O{sub 3} during sintering process. • Fe{sub 3}Si particles were separated by Al{sub 2}O{sub 3} with tunable thickness in composite cores. • Fe{sub 3}Si/Al{sub 2}O{sub 3} had lower core loss and better frequency stability than FeSiAl core. • The insulating layer between ferromagnetic particles can reduce core loss. - Abstract: FeSiAl/SiO{sub 2} core–shell particles and Fe{sub 3}Si/Al{sub 2}O{sub 3} composite cores with tunable insulating layer thicknesses have been synthesized via a modified Stöber method combined with following high temperature sintering process. Most of the conductive FeSiAl particles could be coated by insulating SiO{sub 2} using the modified Stöber method. During the sintering process, the reaction 4Al + 3SiO{sub 2} ≣ 2α-Al{sub 2}O{sub 3} + 3Si took place and the new Fe{sub 3}Si/Al{sub 2}O{sub 3} composite was formed. The Fe{sub 3}Si/Al{sub 2}O{sub 3} composite cores displayed more excellent soft magnetic properties, better frequency stability at high frequencies, much higher resistivity and lower core loss than the raw FeSiAl core. Based on this, several types of FeSiAl/SiO{sub 2} particles and Fe{sub 3}Si/Al{sub 2}O{sub 3} composite cores with tunable insulating layer thicknesses were selectively prepared by simply varying TEOS contents. The thickness of Al{sub 2}O{sub 3} insulating layer and resistivity of Fe{sub 3}Si/Al{sub 2}O{sub 3} composite cores increased with increasing the TEOS contents, while the permeability and core loss changed in the opposite direction.

  14. The role of the PHP domain associated with DNA polymerase X from Thermus thermophilus HB8 in base excision repair.

    Science.gov (United States)

    Nakane, Shuhei; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

    2012-11-01

    Base excision repair (BER) is one of the most commonly used DNA repair pathways involved in genome stability. X-family DNA polymerases (PolXs) play critical roles in BER, especially in filling single-nucleotide gaps. In addition to a polymerase core domain, bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain with phosphoesterase activity which is also required for BER. However, the role of the PHP domain of PolX in bacterial BER remains unresolved. We found that the PHP domain of Thermus thermophilus HB8 PolX (ttPolX) functions as two types of phosphoesterase in BER, including a 3'-phosphatase and an apurinic/apyrimidinic (AP) endonuclease. Experiments using T. thermophilus HB8 cell lysates revealed that the majority of the 3'-phosphatase and AP endonuclease activities are attributable to the another phosphoesterase in T. thermophilus HB8, endonuclease IV (ttEndoIV). However, ttPolX possesses significant 3'-phosphatase activity in ΔttendoIV cell lysate, indicating possible complementation. Our experiments also reveal that there are only two enzymes that display the 3'-phosphatase activity in the T. thermophilus HB8 cell, ttPolX and ttEndoIV. Furthermore, phenotypic analysis of ΔttpolX, ΔttendoIV, and ΔttpolX/ΔttendoIV using hydrogen peroxide and sodium nitrite supports the hypothesis that ttPolX functions as a backup for ttEndoIV in BER. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. A lateral flow biosensor for detection of single nucleotide polymorphism by circular strand displacement reaction.

    Science.gov (United States)

    Xiao, Zhuo; Lie, Puchang; Fang, Zhiyuan; Yu, Luxin; Chen, Junhua; Liu, Jie; Ge, Chenchen; Zhou, Xuemeng; Zeng, Lingwen

    2012-09-04

    A lateral flow biosensor for detection of single nucleotide polymorphism based on circular strand displacement reaction (CSDPR) has been developed. Taking advantage of high fidelity of T4 DNA ligase, signal amplification by CSDPR, and the optical properties of gold nanoparticles, this assay has reached a detection limit of 0.01 fM.

  16. Comparative analyses of ber (zizyphus) honey with other types of honey

    International Nuclear Information System (INIS)

    Iftikhar, F.; Mehmood, R.

    2007-01-01

    Eight different honey samples were collected from different ecological areas of Pakistan and analyzed for various physico-chemical parameters. The aim was to evaluate the quality, difference in the composition and comparison of Ber/Sidder (Zizyphus spp.) honey with other types of honey. The two samples of Ber honey and six other floral honey i.e., Citrus, mixed (citrus + Justicia), Acacia modesta, multi-flora and mixed (zizyphus + sesamum) were collected from Apis mellifera colonies. The colonies of Apis mellifera foraged on the above-mentioned flora in different ecological areas i.e. ber honey from Bannu and Karak, Citrus and mixed (citrus + Justicia) honey from Mandi Bahauddin, Acacia honey from Peshawar + Islamabad and multi-flora from Lahore. Nine legal parameters of honey quality control were followed. All honey samples were well within the limits of Codex Alimentarius Commission except ber and citrus. The ber honey showed high pH (6.85) and low reducing sugars (67.66%), sucrose (1.0%), free acidity (6.09 meq/kg) and total acidity (7.68 meq/kg). Mixed honey (zizyphus + sesamum) exhibited highest pH (6.88), lowest free acidity (2.80 meq/kg) and total acidity (5.50 meq/kg). Citrus honey was also found high in Hydroxy-methyl-furfural (HMF, 22.75 meql kg). (author)

  17. Average BER analysis of SCM-based free-space optical systems by considering the effect of IM3 with OSSB signals under turbulence channels.

    Science.gov (United States)

    Lim, Wansu; Cho, Tae-Sik; Yun, Changho; Kim, Kiseon

    2009-11-09

    In this paper, we derive the average bit error rate (BER) of subcarrier multiplexing (SCM)-based free space optics (FSO) systems using a dual-drive Mach-Zehnder modulator (DD-MZM) for optical single-sideband (OSSB) signals under atmospheric turbulence channels. In particular, we consider the third-order intermodulation (IM3), a significant performance degradation factor, in the case of high input signal power systems. The derived average BER, as a function of the input signal power and the scintillation index, is employed to determine the optimum number of SCM users upon the designing FSO systems. For instance, when the user number doubles, the input signal power decreases by almost 2 dBm under the log-normal and exponential turbulence channels at a given average BER.

  18. Gene-gene, gene-environment, gene-nutrient interactions and single nucleotide polymorphisms of inflammatory cytokines.

    Science.gov (United States)

    Nadeem, Amina; Mumtaz, Sadaf; Naveed, Abdul Khaliq; Aslam, Muhammad; Siddiqui, Arif; Lodhi, Ghulam Mustafa; Ahmad, Tausif

    2015-05-15

    Inflammation plays a significant role in the etiology of type 2 diabetes mellitus (T2DM). The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury, oxidative stress and beta cell apoptosis in T2DM. Among the recognized markers are interleukin (IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha (TNF-α), C-reactive protein, resistin, adiponectin, tissue plasminogen activator, fibrinogen and heptoglobins. Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance. Many single nucleotide polymorphisms (SNPs) in various genes including those of pro and anti-inflammatory cytokines have been reported as a risk for T2DM. Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups. The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene, gene-environment and gene-nutrient interactions. This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6, TNF-α, resistin and adiponectin in pathogenesis of T2DM.

  19. Association of polycystic ovary syndrome susceptibility single nucleotide polymorphism rs2479106 and PCOS in Caucasian patients with PCOS or hirsutism as referral diagnosis

    DEFF Research Database (Denmark)

    Eriksen, Mette B; Brusgaard, Klaus; Andersen, Marianne

    2012-01-01

    Polycystic ovary syndrome (PCOS) is the most common endocrine disease among premenopausal women. A recent study found association between three single nucleotide polymorphisms (SNPs) and PCOS in a cohort of Han Chinese women.......Polycystic ovary syndrome (PCOS) is the most common endocrine disease among premenopausal women. A recent study found association between three single nucleotide polymorphisms (SNPs) and PCOS in a cohort of Han Chinese women....

  20. Neutron scattering-instrumentation at the upgraded research reactor BER II

    International Nuclear Information System (INIS)

    1991-01-01

    The Berlin Neutron Scattering Centre (BENSC) is a newly created special department of the Hahn-Meitner-Institut, in the framework of which the BER II neutron beam reactor is made available to external users. BENSC is devoted to development, continuous modernisation and maintenance of the scientific instrumets at the BER II and to the support of their users. (orig./HSI)

  1. Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus.

    Science.gov (United States)

    Rogers, Stephanie M; Payton, Mark; Allen, Robert W; Melcher, Ulrich; Carver, Jesse; Fletcher, Jacqueline

    2012-05-17

    The September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV) as a model plant virus. This genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs) within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors. Each WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA. The molecular typing method presented is one tool that could be incorporated into the forensic science tool box after a thorough

  2. Microarray Beads for Identifying Blood Group Single Nucleotide Polymorphisms.

    Science.gov (United States)

    Drago, Francesca; Karpasitou, Katerina; Poli, Francesca

    2009-01-01

    We have developed a high-throughput system for single nucleotide polymorphism (SNP) genotyping of alleles of diverse blood group systems exploiting Luminex technology. The method uses specific oligonucleotide probes coupled to a specific array of fluorescent microspheres and is designed for typing Jk(a)/Jk(b), Fy(a)/Fy(b), S/s, K/k, Kp(a)/Kp(b), Js(a)/Js(b), Co(a)/Co(b) and Lu(a)/Lu(b) alleles. Briefly, two multiplex PCR reactions (PCR I and PCR II) according to the laboratory specific needs are set up. PCR I amplifies the alleles tested routinely, namely Jk(a)/Jk(b), Fy(a)/Fy(b), S/s, and K/k. PCR II amplifies those alleles that are typed less frequently. Biotinylated PCR products are hybridized in a single multiplex assay with the corresponding probe mixture. After incubation with R-phycoerythrin-conjugated streptavidin, the emitted fluorescence is analyzed with Luminex 100. So far, we have typed more than 2,000 subjects, 493 of whom with multiplex assay, and there have been no discrepancies with the serology results other than null and/or weak phenotypes. The cost of consumables and reagents for typing a single biallelic pair per sample is less than EUR 3.-, not including DNA extraction costs. The capability to perform multiplexed reactions makes the method markedly suitable for mass screening of red blood cell alleles. This genotyping approach represents an important tool in transfusion medicine.

  3. Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds.

    Directory of Open Access Journals (Sweden)

    Nedenia Bonvino Stafuzza

    Full Text Available Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose, Gyr, Girolando and Holstein (dairy production. A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs and 3,828,041 insertions/deletions (InDels were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs.

  4. Robust embryo identification using first polar body single nucleotide polymorphism microarray-based DNA fingerprinting.

    Science.gov (United States)

    Treff, Nathan R; Su, Jing; Kasabwala, Natasha; Tao, Xin; Miller, Kathleen A; Scott, Richard T

    2010-05-01

    This study sought to validate a novel, minimally invasive system for embryo tracking by single nucleotide polymorphism microarray-based DNA fingerprinting of the first polar body. First polar body-based assignments of which embryos implanted and were delivered after multiple ET were 100% consistent with previously validated embryo DNA fingerprinting-based assignments. Copyright 2010 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  5. Electronic structure of single crystalline Bi sub 2 (Sr,Ca,La) sub 3 Cu sub 2 O sub 8

    Energy Technology Data Exchange (ETDEWEB)

    Lindberg, P A.P.; Shen, Z X; Dessau, D S; Wells, B O; Borg, A; Mitzi, D B; Lindau, I; Spicer, W E; Kapitulnik, A [Stanford Electronics Labs. and Dept. of Applied Physics, Stanford Univ., CA (USA)

    1989-12-01

    Angle-resolved photoemission experiments on single crystals of Bi{sub 2}(Sr,Ca,La){sub 3}Cu{sub 2}O{sub 8} are reported. The data show a dispersionless behaviour of the valence band states as a function of the perpendicular component of the wave vector (along the c-axis), while as a function of the parallel component (in the a-b plane) clear dispersion occurs. Furthermore, polarization-dependent excitations reveal information on the symmetry of the unoccupied states. (orig.).

  6. Magnetic ordering in single crystals of PrBa sub 2 Cu sub 3 O sub 7 sub - subdelta

    CERN Document Server

    Uma, S; Gmelin, E; Rangarajan, G; Skanthakumar, S; Lynn, J W; Walter, R; Lorenz, T; Büchner, B; Walker, E; Erb, A

    1998-01-01

    Heat capacity measurements on pure but twinned single crystals of PrBa sub 2 Cu sub 3 O sub 7 sub - subdelta reveal a sharp peak at T sub N sup P sup sub T =16.6 K, which according to thermal expansion, neutron diffraction, and magnetic susceptibility measurements originates from an antiferromagnetic ordering of the Pr-ion moments. A modest coupling to the Cu(2) spin system is observed. Below T sub N sup P sup sub T a first-order transition in the magnetic structure of the Pr spin system (at 13.4 K in warming; approx. 11 K in cooling) is found. Field-dependent heat capacity data show anisotropic temperature dependences of the c sub p -peaks and recover a Schottky-like anomaly due to the crystal-field-split ground state of the Pr sup 3 sup +. (author). Letter-to-the-editor

  7. Structural and intrinsic Josephson properties of Bi{sub 2}Sr{sub 2}Ca{sub 1−y}Y{sub y}Cu{sub 2}O{sub 8+δ} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Yamaki, K., E-mail: kyamaki@cc.utsunomiya-u.ac.jp; Murata, K.; Irie, A.

    2016-10-15

    Highlights: • Single crystals of yttrium-doped BSCCO (BSCYCO) were grown by a self-flux method. • T{sub c} and c-axis lattice constant of BSCYCO were controlled by the substitution of Y. • A multibranch structure was observed up to y = 0.10 (Bi{sub 2}Sr{sub 2}Ca{sub 1−y}Y{sub y}Cu{sub 2}O{sub 8+δ}). • The BSCYCO mesa has higher maximum voltage compared with nondoped BSCCO. - Abstract: In this study, Bi{sub 2}Sr{sub 2}Ca{sub 1−y}Y{sub y}Cu{sub 2}O{sub 8+δ} (BSCYCO) single crystals with yttrium doping content of y = 0–0.30 were synthesized by a self-flux method. The critical temperature and c-axis lattice constant of BSCYCO were controlled by the substitution of yttrium at the calcium site. A 290 × 90 × 0.4 µm{sup 3} mesa structure was fabricated using photolithography and argon-ion milling. A multibranch structure in current–voltage characteristics was successfully observed for mesas of BSCYCO (y = 0–0.10). The critical current of intrinsic Josephson junctions (IJJs) in BSCYCO mesas was systematically investigated.

  8. Purification of the active C5a receptor from human polymorphonuclear leukocytes as a receptor - G sub i complex

    Energy Technology Data Exchange (ETDEWEB)

    Rollins, T.E.; Siciliano, S.; Kobayashi, S.; Cianciarulo, D.N.; Bonilla-Argudo, V.; Collier, K.; Springer, M.S. (Merck Sharp and Dohme Research Lab., Rahway, NJ (United States))

    1991-02-01

    The authors have isolated, in an active state, the C5a receptor from human polymorphonuclear leukocytes. The purification was achieved in a single step using a C5a affinity column in which the C5a molecule was coupled to the resin through its N terminus. The purified receptor, like the crude solubilized molecule, exhibited a single class of high-affinity binding sites with a K{sub d} of 30 pM. Further, the binding of C5a retained its sensitivity to guanine nucleotides, implying that the purified receptor contained a guanine nucleotide-binding protein (G protein). SDS/PAGE revealed the presence of three polypeptides with molecular masses of 42, 40, and 36 kDa, which were determined to be the C5a-binding subunit and the {alpha} and {beta} subunits of G{sub i}, respectively. The 36- and 40-kDa polypeptides were identified by immunoblotting and by the ability of pertussis toxin to ADP-ribosylate the 40-kDa molecule. These results confirm their earlier hypothesis that the receptor exists as a complex with a G protein in the presence or absence of C5a. The tight coupling between the receptor and G protein should make possible the identification of the G protein(s) involved in the transduction pathways used by C5a to produce its many biological effects.

  9. Meta-analysis of the relationship between single nucleotide polymorphism of IL-10-1082G/A and rheumatic heart disease.

    Science.gov (United States)

    Dai, Weiran; Ye, Ziliang; Lu, Haili; Su, Qiang; Li, Hui; Li, Lang

    2018-02-23

    The results showed that there was a certain correlation between the single nucleotide polymorphism of IL-10-1082G/A and rheumatic heart disease, but there was no systematic study to verify this conclusion. Systematic review of the association between single nucleotide polymorphism of IL-10-1082G/A locus and rheumatic heart disease. Computer retrieval PubMed, EMbase, Cochrane Library, CBM, CNKI, VIP and Data WanFang, the retrieval time limit from inception to June 2017. A case control study of single nucleotide polymorphisms and rheumatic heart disease in patients with rheumatic heart disease in the IL-10-1082G/A was collected. Two researchers independently screened the literature, extracted data and evaluated the risk of bias in the study, and using RevMan5.3 software for data analysis. A total of 3 case control studies were included, including 318 patients with rheumatic heart disease and 502 controls. Meta-analysis showed that there was no correlation between IL-10-1082G/A gene polymorphism and rheumatic heart disease [AA+AG VS GG: OR = 0.62, 95% CI (0.28, 1.39), P = 0.25; AA VS AG+GG: OR = 0.73, 95% CI (0.54, 1.00), P = 0.05; AA VS GG: OR = 0.70, 95% CI(0.47, 1.05), P = 0.08; AG VS GG: OR = 0.65, 95% CI (0.22, 1.92), P = 0.43; A VS G: OR = 0.87, 95% CI (0.71, 1.06), P = 0.17]. When AA is a recessive gene, the single nucleotide polymorphism of IL-10-1082G/A is associated with the presence of rheumatic heart disease. Due to the limitations of the quantity and quality of the included literatures, the further research results were still needed.

  10. Association of single nucleotide polymorphism in CD28(C/T-I3 + 17) and CD40 (C/T-1) genes with the Graves' disease.

    Science.gov (United States)

    Mustafa, Saima; Fatima, Hira; Fatima, Sadia; Khosa, Tafheem; Akbar, Atif; Shaikh, Rehan Sadiq; Iqbal, Furhan

    2018-01-01

    To find out a correlation between the single nucleotide polymorphisms in cluster of differentiation 28 and cluster of differentiation 40 genes with Graves' disease, if any. This case-control study was conducted at the Multan Institute of Nuclear Medicine and Radiotherapy, Multan, Pakistan, and comprised blood samples of Graves' disease patients and controls. Various risk factors were also correlated either with the genotype at each single-nucleotide polymorphism or with various combinations of genotypes studied during present investigation. Of the 160 samples, there were 80(50%) each from patients and controls. Risk factor analysis revealed that gender (p=0.008), marital status (pGraves' disease. Both single-nucleotide polymorphisms in both genes were not associated with Graves' disease, either individually or in any combined form.

  11. Magnetic properties of single crystalline Mn{sub 4}Si{sub 7}

    Energy Technology Data Exchange (ETDEWEB)

    Gottlieb, U.; Sulpice, A.; Lambert-Andron, B.; Laborde, O

    2003-10-27

    A single crystal of MnSi{sub 2-x} was obtained by a modified Czochralski pulling technique in a cold copper crucible. The quality and the nature of the sample were checked by an accurate crystal structure determination, which revealed the sample to be Mn{sub 4}Si{sub 7}. Resistivity and magnetic measurements were performed on this sample in the temperature range between 2 K and room temperature and in magnetic fields up to 7.5 T. Mn{sub 4}Si{sub 7} shows a metallic behaviour and the good crystal quality was revealed by the high residual resistance ratio of 360. For the magnetic susceptibility we observed a Curie-Weiss law above about 40 K with a low effective moment of p{sub eff}=0.365 {mu}{sub B}/Mn. Below this temperature, moments order in an anisotropic helical state, and in fields above 1 T, they align with a saturation moment of p{sub sat}=0.012 {mu}{sub B}/Mn. Mn{sub 4}Si{sub 7} is a weak itinerant magnetic system that could be a good candidate for the observation of the critical quantum fluctuations expected for marginal Fermi liquids.

  12. Effect of gamma irradiation on antioxidant properties of ber (Zizyphus mauritiana) fruit

    International Nuclear Information System (INIS)

    Kavitha, C.; Kuna, Aparna; Sagar, S.B.; Padmavati, T.V.N.; Supraja, T.; Prabhakar, N.

    2015-01-01

    Effect of gamma irradiation (0.25 to 1.0kGy) on antioxidant properties of ber fruit was studied. Antioxidant properties of ber fruits were determined by scavenging DPPH radical activity, reducing power assay, super oxide anion radical activity, TBARS, total phenolic content and total flavonoid content. Gamma irradiation treatment up to 1.0 kGy elevated the scavenging DPPH radical activity (9 %), super oxide anion radical activity (26 %) and total flavonoid content (208 %) compared to fresh ber fruit. On the other hand it brought down the reducing power activity (65 %) and total phenolic content (18 %) as compared to raw fruit. The TBARS activity statistically increased upon irradiation of ber fruit. It indicated that total antioxidant activity decreased as TBARS value increased. Therefore 0.25 to 0.5kGy is better dose to retain the natural antioxidant in fruit. (author)

  13. Identification of a single-nucleotide insertion in the promoter region affecting the sodC promoter activity in Brucella neotomae.

    Directory of Open Access Journals (Sweden)

    Dina A Moustafa

    Full Text Available Brucella neotomae is not known to be associated with clinical disease in any host species. Previous research suggested that B. neotomae might not express detectable levels of Cu/Zn superoxide dismutase (SOD, a periplasmic enzyme known to be involved in protecting Brucella from oxidative bactericidal effects of host phagocytes. This study was undertaken to investigate the genetic basis for the disparity in SOD expression in B. neotomae. Our Western blot and SOD enzyme assay analyses indicated that B. neotomae does express SOD, but at a substantially reduced level. Nucleotide sequence analysis of region upstream to the sodC gene identified a single-nucleotide insertion in the potential promoter region. The same single-nucleotide insertion was also detected in the sodC promoter of B. suis strain Thomsen, belonging to biovar 2 in which SOD expression was undetectable previously. Examination of the sodC promoter activities using translational fusion constructs with E. coli β-galactosidase demonstrated that the B. neotomae and B. suis biovar 2 promoters were very weak in driving gene expression. Site-directed mutation studies indicated that the insertion of A in the B. neotomae sodC promoter reduced the promoter activity. Increasing the level of SOD expression in B. neotomae through complementation with B. abortus sodC gene did not alter the bacterial survival in J774A.1 macrophage-like cells and in tissues of BALB/c and C57BL/6 mice. These results for the first time demonstrate the occurrence of a single-nucleotide polymorphism affecting promoter function and gene expression in Brucella.

  14. Analysis of multiple single nucleotide polymorphisms (SNP) on DNA traces from plasma and dried blood samples

    NARCIS (Netherlands)

    Catsburg, Arnold; van der Zwet, Wil C.; Morre, Servaas A.; Ouburg, Sander; Vandenbroucke-Grauls, Christina M. J. E.; Savelkoul, Paul H. M.

    2007-01-01

    Reliable analysis of single nucleotide polymorphisms (SNPs) in DNA derived from samples containing low numbers of cells or from suboptimal sources can be difficult. A new procedure to characterize multiple SNPs in traces of DNA from plasma and old dried blood samples was developed. Six SNPs in the

  15. Single nucleotide polymorphism discrimination with and without an ethidium bromide intercalator.

    Science.gov (United States)

    Fenati, Renzo A; Connolly, Ashley R; Ellis, Amanda V

    2017-02-15

    Single nucleotide polymorphism (SNP) genotyping is an important aspect in understanding genetic variations. Here, we discriminate SNPs using toe-hold mediated displacement reactions. The biological target is an 80 nucleotide long double-stranded-DNA from the mtDNA HV1 region, associated with maternal ancestry. This target has been specially designed with a pendant toehold and a cationic fluorophore, ATTO 647N, as a reporter, produced in a polymerase chain reaction. Rates of reaction for the toehold-polymerase chain reaction products (TPPs) with their corresponding complementary displacing sequences, labelled with a Black Hole Quencher 1, followed the order TPP-Cytosine > TPP-Thymine > TPP-Adenine ≥ TPP-Guanine. Non-complementary rates were the slowest with mismatches involving cytosine. These reactions, operating in a static/or contact mode, gave averaged readouts between SNPs within 15 min (with 80-90% quenching), compared to 25-30 min in previous studies involving fluorescence resonance energy transfer. Addition of an intercalating agent, ethidium bromide, retarded the rate of reaction in which cytosine was involved, presumably through stabilization of the base pairing, which resulted in markedly improved discrimination of cytosine containing SNPs. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Ewing's sarcoma: analysis of single nucleotide polymorphism in the EWS gene.

    Science.gov (United States)

    Silva, Deborah S B S; Sawitzki, Fernanda R; De Toni, Elisa C; Graebin, Pietra; Picanco, Juliane B; Abujamra, Ana Lucia; de Farias, Caroline B; Roesler, Rafael; Brunetto, Algemir L; Alho, Clarice S

    2012-11-10

    We aimed to investigate single nucleotide polymorphisms (SNPs) in the EWS gene breaking region in order to analyze Ewing's sarcoma susceptibility. The SNPs were investigated in a healthy subject population and in Ewing's sarcoma patients from Southern Brazil. Genotyping was performed by TaqMan® assay for allelic discrimination using Real-Time PCR. The analysis of incidence of SNPs or different SNP-arrangements revealed a higher presence of homozygote TT-rs4820804 in Ewing's sarcoma patients (p=0.02; Chi Square Test). About 300 bp from the rs4820804 SNP lies a palindromic hexamer (5'-GCTAGC-3') and three nucleotides (GTC), which were previously identified to be in close vicinity of the breakpoint junction in both EWS and FLI1 genes. This DNA segment surrounding the rs4820804 SNP is likely to indicate a breakpoint region. If the T-rs4820804 allele predisposes a DNA fragment to breakage, homozygotes (TT-rs4820804) would have double the chance of having a chromosome break, increasing the chances for a translocation to occur. In conclusion, the TT-rs4820804 EWS genotype can be associated with Ewing's sarcoma and the SNP rs4820804 can be a candidate marker to understand Ewing's sarcoma susceptibility. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Magnetic, transport, and optical properties of Ca{sub 0.85}Eu{sub 0.15}MnO{sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Naumov, S.V., E-mail: naumov@imp.uran.ru [Institute of Metal Physics, Ural Branch of RAS, Kovalevskaya Street 18, Ekaterinburg 620990 (Russian Federation); Loshkareva, N.N.; Mostovshchikova, E.V.; Solin, N.I.; Korolev, A.V.; Arbuzova, T.I.; Telegin, S.V.; Patrakov, E.I. [Institute of Metal Physics, Ural Branch of RAS, Kovalevskaya Street 18, Ekaterinburg 620990 (Russian Federation)

    2013-01-01

    Magnetic, transport and optical properties of the Ca{sub 0.85}Eu{sub 0.15}MnO{sub 3} single crystal are studied and discussed in comparison with the properties of polycrystalline sample. The magnetic data show existence the two magnetic phase transitions under cooling: the transition near 150 K occurs from the paramagnetic orthorhombic to C-type antiferromagnetic monoclinic phase with the charge/orbital ordering in some part of the crystal; and at 90 K the transition from the paramagnetic to G-type antiferromagnetic phase takes place in another part of the crystal with the orthorhombic structure. The magnetoresistance of the Ca{sub 0.85}Eu{sub 0.15}MnO{sub 3} single crystal has features at temperatures of these phase transitions. Differences in the properties of single crystal and polycrystalline sample with the same content of Eu are associated with the ordering of oxygen vacancies that appear under the crystal growth. The reflection spectra in infrared range confirm the existence of the electron conductivity in a narrow band at room temperature.

  18. Rapid synthesis and catalytic performance of {alpha}-Mn{sub 2}O{sub 3} single-crystal nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Xinsong; Hu, Xingming; Zhu, Jinmiao; Dong, Huaze; Wang, Yanping [Department of Chemistry and Chemical Engineering, Hefei Normal University, Hefei 230061 (China); Yang, Baojun [Anhui Key Laboratory of Controllable Chemistry Reaction and Material Chemical Engineering, School of Chemical Engineering, Hefei University of Technology, Hefei 230009 (China); Hao, Jianwen [Department of Chemical Engineering, Anhui Vocational and Technical College, Hefei 230051 (China)

    2011-12-15

    Single-crystal {alpha}-Mn{sub 2}O{sub 3} nanowires were prepared via a ''self-sacrificing template'' route, simply by calcining the prepared {alpha}-MnO{sub 2} nanowire precursors at 550 C for 1.5 h. XRD, TEM, SEM and HRTEM characterizations show that the as-prepared {alpha}-Mn{sub 2}O{sub 3} samples are all phase pure and the nanowires have uniform diameters of approximately 15-30 nm and lengths up to several micrometers. The catalytic performances of the prepared {alpha}-Mn{sub 2}O{sub 3} nanowires were studied in the degradation of coking wastewater with H{sub 2}O{sub 2} as the oxidant, and the technological conditions were optimized by single-factor and orthogonal experiments. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  19. Do berço ao berçário: a instituição como morada e lugar de contato

    Directory of Open Access Journals (Sweden)

    Marta Nörnberg

    2013-12-01

    Full Text Available Este ensaio aborda o sentido da instituição infantil a partir de uma perspectiva ético-estético-afetiva do viver humano. A abordagem ampara-se em perspectivas filosóficas sobre a existência humana. Os argumentos apresentam o berçário como morada, lugar do viver juntos, instituição que se faz em coletividade, nela e com ela, decorrente do encontro de bebês e adultos. Ao constituir-se como morada dos bebês, o berçário ritualiza e reatualiza a prática pedagógica como lugar de relação entre bebês e adultos, requerendo uma pedagogia do contato.

  20. Caveolin-1 single nucleotide polymorphism in antineutrophil cytoplasmic antibody associated vasculitis.

    Directory of Open Access Journals (Sweden)

    Sourabh Chand

    Full Text Available Immunosuppression is cornerstone treatment of antineutrophil cytoplasmic antibody associated vasculitis (AAV but is later complicated by infection, cancer, cardiovascular and chronic kidney disease. Caveolin-1 is an essential structural protein for small cell membrane invaginations known as caveolae. Its functional role has been associated with these complications. For the first time, caveolin-1 (CAV1 gene variation is studied in AAV.CAV1 single nucleotide polymorphism rs4730751 was analysed in genomic DNA from 187 white patients with AAV from Birmingham, United Kingdom. The primary outcome measure was the composite endpoint of time to all-cause mortality or renal replacement therapy. Secondary endpoints included time to all-cause mortality, death from sepsis or vascular disease, cancer and renal replacement therapy. Validation of results was sought from 589 white AAV patients, from two European cohorts.The primary outcome occurred in 41.7% of Birmingham patients. In a multivariate model, non-CC genotype variation at the studied single nucleotide polymorphism was associated with increased risk from: the primary outcome measure [HR 1.86; 95% CI: 1.14-3.04; p=0.013], all-cause mortality [HR:1.83; 95% CI: 1.02-3.27; p=0.042], death from infection [HR:3.71; 95% CI: 1.28-10.77; p=0.016], death from vascular disease [HR:3.13; 95% CI: 1.07-9.10; p=0.037], and cancer [HR:5.55; 95% CI: 1.59-19.31; p=0.007]. In the validation cohort, the primary outcome rate was far lower (10.4%; no association between genotype and the studied endpoints was evident.The presence of a CC genotype in Birmingham is associated with protection from adverse outcomes of immunosuppression treated AAV. Lack of replication in the European cohort may have resulted from low clinical event rates. These findings are worthy of further study in larger cohorts.

  1. Transmembrane Domain Single-Nucleotide Polymorphisms Impair Expression and Transport Activity of ABC Transporter ABCG2

    NARCIS (Netherlands)

    Sjostedt, N.; Heuvel, J.J.M.W. van den; Koenderink, J.B.; Kidron, H.

    2017-01-01

    PURPOSE: To study the function and expression of nine naturally occurring single-nucleotide polymorphisms (G406R, F431L, S441N, P480L, F489L, M515R, L525R, A528T and T542A) that are predicted to reside in the transmembrane regions of the ABC transporter ABCG2. METHODS: The transport activity of the

  2. Few single nucleotide variations in exomes of human cord blood induced pluripotent stem cells.

    Directory of Open Access Journals (Sweden)

    Rui-Jun Su

    Full Text Available The effect of the cellular reprogramming process per se on mutation load remains unclear. To address this issue, we performed whole exome sequencing analysis of induced pluripotent stem cells (iPSCs reprogrammed from human cord blood (CB CD34(+ cells. Cells from a single donor and improved lentiviral vectors for high-efficiency (2-14% reprogramming were used to examine the effects of three different combinations of reprogramming factors: OCT4 and SOX2 (OS, OS and ZSCAN4 (OSZ, OS and MYC and KLF4 (OSMK. Five clones from each group were subject to whole exome sequencing analysis. We identified 14, 11, and 9 single nucleotide variations (SNVs, in exomes, including untranslated regions (UTR, in the five clones of OSMK, OS, and OSZ iPSC lines. Only 8, 7, and 4 of these, respectively, were protein-coding mutations. An average of 1.3 coding mutations per CB iPSC line is remarkably lower than previous studies using fibroblasts and low-efficiency reprogramming approaches. These data demonstrate that point nucleotide mutations during cord blood reprogramming are negligible and that the inclusion of genome stabilizers like ZSCAN4 during reprogramming may further decrease reprogramming-associated mutations. Our findings provide evidence that CB is a superior source of cells for iPSC banking.

  3. Vertical Bridgman growth and characterization of Cd<sub>0.95-xsub>MnxZn>0.05sub>Te (x=0.20, 0.30) single-crystal ingots

    Energy Technology Data Exchange (ETDEWEB)

    Bolotnikov, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Kopach, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Kopach, O. [Brookhaven National Lab. (BNL), Upton, NY (United States); Shcherbak, L. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fochuk, P. [Brookhaven National Lab. (BNL), Upton, NY (United States); Filonenko, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); James, R. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2017-08-01

    Solid-liquid phase transitions in Cd<sub>0.95-xsub>MnxZn>0.05sub>Te alloys with x = 0.20 and 0.30 were investigated by differential thermal analysis (DTA). The heating/cooling rates were 5 and 10 K/min with a melt dwell time of 10, 30 and 60 minutes. Cd<sub>0.95-xsub>MnxZn>0.05sub>Te (x=0.20, 0.30) single-crystal ingots were grown by the vertical Bridgman method guided using the DTA results. Te inclusions (1-20 microns), typical for CdTe and Cd(Zn)Te crystals, were observed in the ingots by infrared transmission microscopy. The measured X-ray diffraction patterns showed that all compositions are found to be in a single phase. Using current-voltage (I-V) measurements, the resistivity of the samples from each ingot was estimated to be about 105 Ohm·cm. The optical transmission analysis demonstrated that the band-gap width of the investigated ingots increased from 1.77 to 1.88 eV with the increase of the MnTe content from 20 to 30 mol. %.

  4. Assembling a dual purpose TaqMan-based panel of single-nucleotide polymorphism markers in rainbow trout and steelhead (Oncorhynchus mykiss) for association mapping and population genetics analysis

    DEFF Research Database (Denmark)

    Hansen, Mette H H; Young, Sewall; Jørgensen, Hanne Birgitte Hede

    2011-01-01

    We establish a TaqMan-based assay panel for genotyping single-nucleotide polymorphisms in rainbow trout and steelhead (Oncorhynchus mykiss). We develop 22 novel single-nucleotide polymorphism markers based on new steelhead sequence data and on assays from sister taxa. Additionally, we adapt 154 p...

  5. Single-crystal structure refinement of YbF{sub 2} with a remark about YbH{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Reckeweg, Olaf; DiSalvo, Francis J. [Cornell Univ., Ithaca, NY (United States). Dept. of Chemistry and Chemical Biology

    2017-07-01

    Transparent-yellow single crystals of YbF{sub 2} were obtained as only crystalline product from the solid-state reaction of Yb and teflon designed to yield 'Yb{sub 3}C{sub 3}F{sub 2}' in addition to some amorphous black material. The first single-crystal structure determination of YbF{sub 2} (cubic space group Fm anti 3m, CaF{sub 2}-type structure, a = 559.46(16) pm; R1 = 1.2%, wR2 = 3.2%) was the starting point to compare isostructural binary fluorides MF{sub 2} and hydrides MH{sub 2} (M = Ca, Yb, Eu, Sr and Ba) exhibiting an as-yet unexplained small volume per formula unit for YbH{sub 2}.

  6. Evidence for single nucleotide polymorphisms and their association with bipolar disorder

    Directory of Open Access Journals (Sweden)

    Szczepankiewicz A

    2013-10-01

    Full Text Available Aleksandra Szczepankiewicz1,21Laboratory of Molecular and Cell Biology, 2Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, PolandAbstract: Bipolar disorder (BD is a complex disorder with a number of susceptibility genes and environmental risk factors involved in its pathogenesis. In recent years, huge progress has been made in molecular techniques for genetic studies, which have enabled identification of numerous genomic regions and genetic variants implicated in BD across populations. Despite the abundance of genetic findings, the results have often been inconsistent and not replicated for many candidate genes/single nucleotide polymorphisms (SNPs. Therefore, the aim of the review presented here is to summarize the most important data reported so far in candidate gene and genome-wide association studies. Taking into account the abundance of association data, this review focuses on the most extensively studied genes and polymorphisms reported so far for BD to present the most promising genomic regions/SNPs involved in BD. The review of association data reveals evidence for several genes (SLC6A4/5-HTT [serotonin transporter gene], BDNF [brain-derived neurotrophic factor], DAOA [D-amino acid oxidase activator], DTNBP1 [dysbindin], NRG1 [neuregulin 1], DISC1 [disrupted in schizophrenia 1] to be crucial candidates in BD, whereas numerous genome-wide association studies conducted in BD indicate polymorphisms in two genes (CACNA1C [calcium channel, voltage-dependent, L type, alpha 1C subunit], ANK3 [ankyrin 3] replicated for association with BD in most of these studies. Nevertheless, further studies focusing on interactions between multiple candidate genes/SNPs, as well as systems biology and pathway analyses are necessary to integrate and improve the way we analyze the currently available association data.Keywords: candidate gene, genome-wide association study, SLC6A4, BDNF, DAOA, DTNBP1, NRG1, DISC1

  7. Neue Werkstoffe über additive Fertigung

    OpenAIRE

    Günther, Johannes; Niendorf, Thomas

    2016-01-01

    Über die additive Fertigung, oftmals bezeichnet als 3D-Druck, lassen sich Bauteile nahezu beliebiger geometrischer Komplexität herstellen. Gleichzeitig lassen die Prozessrandbedingungen die direkte Einstellung der Mikrostruktur in den verwendeten metallischen Werkstoffen zu. Hieraus ergeben sich weitreichende Möglichkeiten bezüglich der Eigenschaftsoptimierung aktueller Hochleistungswerkstoffe.

  8. The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara Elizabeth

    2016-05-11

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

  9. BiI{sub 3} single crystal for room-temperature gamma ray detectors

    Energy Technology Data Exchange (ETDEWEB)

    Saito, T., E-mail: saito.tatsuya125@canon.co.jp [Frontier Research Center, Canon Inc., 3-30-2, Shimomaruko, Ohta-ku, Tokyo 146-8501 (Japan); Iwasaki, T. [Frontier Research Center, Canon Inc., 3-30-2, Shimomaruko, Ohta-ku, Tokyo 146-8501 (Japan); Kurosawa, S.; Yoshikawa, A. [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577 (Japan); New Industry Creation Hatchery Center (NICHe), Tohoku University, 6-6-10 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 (Japan); Den, T. [Frontier Research Center, Canon Inc., 3-30-2, Shimomaruko, Ohta-ku, Tokyo 146-8501 (Japan)

    2016-01-11

    BiI{sub 3} single crystals were grown by the physical vapor transport method. The repeated sublimation of the starting material reduced impurities in the BiI{sub 3} single crystal to sub-ppm levels. The detector was fabricated by depositing Au electrodes on both surfaces of the 100-μm-thick BiI{sub 3} single crystal platelet. The resistivity of the BiI{sub 3} single crystal was increased by post-annealing in an iodine atmosphere (ρ=1.6×10{sup 11} Ω cm). Pulse height spectroscopy measurements showed clear peaks in the energy spectrum of alpha particles or gamma rays. It was estimated that the mobility-lifetime product was μ{sub e}τ{sub e}=3.4–8.5×10{sup −6} cm{sup 2}/V and the electron–hole pair creation energy was 5.8 eV. Our results show that BiI{sub 3} single crystals are promising candidates for detectors used in radiographic imaging or gamma ray spectroscopy.

  10. Ein Lehrbuch über Psychiatrie und Psychotherapie – Geschlechtsunterschiede unter der Lupe?

    Directory of Open Access Journals (Sweden)

    Isabella Heuser

    2007-07-01

    Full Text Available Anke Rohde und Andreas Marneros haben sich ein hohes Ziel gesetzt: ein übersichtliches Lehrbuch für Psychiatrie und Psychotherapie, das erstmals eine systematische Zusammenstellung des Wissens über geschlechtsspezifische Aspekte von Symptomatologie, Epidemiologie, Diagnostik, Pharmakotherapie und Psychotherapie psychischer Störungen enthält. Bemerkenswert ist dabei zweierlei: Erstens werden bei der Betrachtung geschlechtsspezifischer Unterschiede im Sinne der Genderforschung Frauen und Männer berücksichtigt, zweitens wird ein vollständiger Überblick sowohl über die häufigen und bekannten psychischen Störungen als auch die äußerst seltenen psychiatrischen Erkrankungen der gesamten Altersspanne gegeben. Wenngleich die Qualität der einzelnen Beiträge deutlich zwischen sehr differenzierter und leider auch für ein Handbuch eindeutig zu oberflächlicher Betrachtung variiert, liegt in dem Band ein weitgehend informatives Nachschlagewerk vor, das einen ersten Überblick über die geschlechtsspezifische Psychiatrie gibt.

  11. Single nucleotide editing without DNA cleavage using CRISPR/Cas9-deaminase in the sea urchin embryo.

    Science.gov (United States)

    Shevidi, Saba; Uchida, Alicia; Schudrowitz, Natalie; Wessel, Gary M; Yajima, Mamiko

    2017-12-01

    A single base pair mutation in the genome can result in many congenital disorders in humans. The recent gene editing approach using CRISPR/Cas9 has rapidly become a powerful tool to replicate or repair such mutations in the genome. These approaches rely on cleaving DNA, while presenting unexpected risks. In this study, we demonstrate a modified CRISPR/Cas9 system fused to cytosine deaminase (Cas9-DA), which induces a single nucleotide conversion in the genome. Cas9-DA was introduced into sea urchin eggs with sgRNAs targeted for SpAlx1, SpDsh, or SpPks, each of which is critical for skeletogenesis, embryonic axis formation, or pigment formation, respectively. We found that both Cas9 and Cas9-DA edit the genome, and cause predicted phenotypic changes at a similar efficiency. Cas9, however, resulted in significant deletions in the genome centered on the gRNA target sequence, whereas Cas9-DA resulted in single or double nucleotide editing of C to T conversions within the gRNA target sequence. These results suggest that the Cas9-DA approach may be useful for manipulating gene activity with decreased risks of genomic aberrations. Developmental Dynamics 246:1036-1046, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  12. The Role of Cyclic Nucleotide Signaling Pathways in Cancer: Targets for Prevention and Treatment

    Energy Technology Data Exchange (ETDEWEB)

    Fajardo, Alexandra M.; Piazza, Gary A. [Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Ave, Suite 3029, Mobile, AL 36604 (United States); Tinsley, Heather N., E-mail: htinsley@montevallo.edu [Department of Biology, Chemistry, and Mathematics, University of Montevallo, Station 6480, Montevallo, AL 35115 (United States)

    2014-02-26

    For more than four decades, the cyclic nucleotides cyclic AMP (cAMP) and cyclic GMP (cGMP) have been recognized as important signaling molecules within cells. Under normal physiological conditions, cyclic nucleotides regulate a myriad of biological processes such as cell growth and adhesion, energy homeostasis, neuronal signaling, and muscle relaxation. In addition, altered cyclic nucleotide signaling has been observed in a number of pathophysiological conditions, including cancer. While the distinct molecular alterations responsible for these effects vary depending on the specific cancer type, several studies have demonstrated that activation of cyclic nucleotide signaling through one of three mechanisms—induction of cyclic nucleotide synthesis, inhibition of cyclic nucleotide degradation, or activation of cyclic nucleotide receptors—is sufficient to inhibit proliferation and activate apoptosis in many types of cancer cells. These findings suggest that targeting cyclic nucleotide signaling can provide a strategy for the discovery of novel agents for the prevention and/or treatment of selected cancers.

  13. BER performance comparison of optical CDMA systems with/without turbo codes

    Science.gov (United States)

    Kulkarni, Muralidhar; Chauhan, Vijender S.; Dutta, Yashpal; Sinha, Ravindra K.

    2002-08-01

    In this paper, we have analyzed and simulated the BER performance of a turbo coded optical code-division multiple-access (TC-OCDMA) system. A performance comparison has been made between uncoded OCDMA and TC-OCDMA systems employing various OCDMA address codes (optical orthogonal codes (OOCs), Generalized Multiwavelength Prime codes (GMWPC's), and Generalized Multiwavelength Reed Solomon code (GMWRSC's)). The BER performance of TC-OCDMA systems has been analyzed and simulated by varying the code weight of address code employed by the system. From the simulation results, it is observed that lower weight address codes can be employed for TC-OCDMA systems that can have the equivalent BER performance of uncoded systems employing higher weight address codes for a fixed number of active users.

  14. BER Science Network Requirements Workshop -- July 26-27,2007

    Energy Technology Data Exchange (ETDEWEB)

    Tierney, Brian L.; Dart, Eli

    2008-02-01

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the US Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States of America. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In July 2007, ESnet and the Biological and Environmental Research (BER) Program Office of the DOE Office of Science organized a workshop to characterize the networking requirements of the science programs funded by the BER Program Office. These included several large programs and facilities, including Atmospheric Radiation Measurement (ARM) Program and the ARM Climate Research Facility (ACRF), Bioinformatics and Life Sciences Programs, Climate Sciences Programs, the Environmental Molecular Sciences Laboratory at PNNL, the Joint Genome Institute (JGI). National Center for Atmospheric Research (NCAR) also participated in the workshop and contributed a section to this report due to the fact that a large distributed data repository for climate data will be established at NERSC, ORNL and NCAR, and this will have an effect on ESnet. Workshop participants were asked to codify their requirements in a 'case study' format, which summarizes the instruments and facilities necessary for the science and the process by which the science is done, with emphasis on the network services needed and the way in which the network is used. Participants were asked to consider three time scales in their case studies--the near term (immediately and up to 12 months in the future), the medium term (3-5 years in the future), and the long term (greater than 5 years in the future). In addition to achieving its goal of collecting and

  15. Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks

    OpenAIRE

    Zhao, Huiying; Nyholt, Dale R.; Yang, Yuanhao; Wang, Jihua; Yang, Yuedong

    2017-01-01

    Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous...

  16. Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus

    Science.gov (United States)

    2012-01-01

    Background The September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV) as a model plant virus. Method This genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs) within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors. Result Each WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA. Conclusion The molecular typing method presented is one tool that could be incorporated into the forensic

  17. Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach

    Directory of Open Access Journals (Sweden)

    Heinz Ruth A

    2008-01-01

    Full Text Available Abstract Background Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs and short insertion and/or deletions (indels to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. Results A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (θ = 0.0056, as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88. Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2, with a large proportion of the inbred lines being assigned to one of them (G1. Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance. Conclusion Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop

  18. Imputation of single nucleotide polymorhpism genotypes of Hereford cattle: reference panel size, family relationship and population structure

    Science.gov (United States)

    The objective of this study is to investigate single nucleotide polymorphism (SNP) genotypes imputation of Hereford cattle. Purebred Herefords were from two sources, Line 1 Hereford (N=240) and representatives of Industry Herefords (N=311). Using different reference panels of 62 and 494 males with 1...

  19. A single nucleotide polymorphism in the promoter of the LOXL1 gene and its relationship to pelvic organ prolapse and preterm premature rupture of membranes.

    Science.gov (United States)

    Ferrell, Georgia; Lu, Minyan; Stoddard, Paul; Sammel, Mary D; Romero, Roberto; Strauss, Jerome F; Matthews, Catherine A

    2009-05-01

    Pelvic organ prolapse and preterm premature rupture of membranes, the 2 conditions which have in common weakening of the tensile strength of tissues, are thought to be caused, in part, by abnormal extracellular matrix synthesis and/or catabolism. We identified a new single nucleotide polymorphism (NT_010194(LOXL1):g.45008784A>C) in the promoter of the LOXL1 gene, which is essential for elastin synthesis. Promoter studies showed that the minor "C'' allele had significantly greater activity than the major "A'' allele. Case-control studies examined the association of the alleles of this single nucleotide polymorphism with pelvic organ prolapse and preterm premature rupture of membranes. When comparing allele frequencies and genotypes in pelvic organ prolapse cases versus controls, no significant associations were found. A case-control study conducted in African American neonates also found no significant associations between the promoter alleles and preterm premature rupture of membranes. We conclude that a functional single nucleotide polymorphism exists in the promoter region of the LOXL1 gene. Association studies suggest that the promoter single nucleotide polymorphism does not contribute significantly to risk of pelvic organ prolapse or preterm premature rupture of membranes.

  20. Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae.

    Science.gov (United States)

    Rosinski-Chupin, Isabelle; Sauvage, Elisabeth; Sismeiro, Odile; Villain, Adrien; Da Cunha, Violette; Caliot, Marie-Elise; Dillies, Marie-Agnès; Trieu-Cuot, Patrick; Bouloc, Philippe; Lartigue, Marie-Frédérique; Glaser, Philippe

    2015-05-30

    Streptococcus agalactiae, or Group B Streptococcus, is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. In an effort to reconstruct the transcriptional networks involved in S. agalactiae physiology and pathogenesis, we performed an extensive and robust characterization of its transcriptome through a combination of differential RNA-sequencing in eight different growth conditions or genetic backgrounds and strand-specific RNA-sequencing. Our study identified 1,210 transcription start sites (TSSs) and 655 transcript ends as well as 39 riboswitches and cis-regulatory regions, 39 cis-antisense non-coding RNAs and 47 small RNAs potentially acting in trans. Among these putative regulatory RNAs, ten were differentially expressed in response to an acid stress and two riboswitches sensed directly or indirectly the pH modification. Strikingly, 15% of the TSSs identified were associated with the incorporation of pseudo-templated nucleotides, showing that reiterative transcription is a pervasive process in S. agalactiae. In particular, 40% of the TSSs upstream genes involved in nucleotide metabolism show reiterative transcription potentially regulating gene expression, as exemplified for pyrG and thyA encoding the CTP synthase and the thymidylate synthase respectively. This comprehensive map of the transcriptome at the single nucleotide resolution led to the discovery of new regulatory mechanisms in S. agalactiae. It also provides the basis for in depth analyses of transcriptional networks in S. agalactiae and of the regulatory role of reiterative transcription following variations of intra-cellular nucleotide pools.

  1. [A population genetic study of 22 autosomal loci of single nucleotide polymorphisms].

    Science.gov (United States)

    Tang, Jian-pin; Jiang, Feng-hui; Shi, Mei-sen; Xu, Chuan-chao; Chen, Rui; Lai, Xiao-pin

    2012-12-01

    To evaluate polymorphisms and forensic efficiency of 22 non-binary single nucleotide polymorphism (SNP) loci. One hundred ethnic Han Chinese individuals were recruited from Dongguan, Guangdong. The 22 loci were genotyped with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Nine loci were found with a single allele, 4 loci were found to be biallelic, whilst 9 loci were found to have 3 alleles. For 13 polymorphic loci, the combined discrimination power and power of exclusion were 0.999 98 and 0.9330, respectively. For the 9 non-biallelic loci, the combined discrimination power and power of exclusion were 0.9998 and 0.8956, respectively. For motherless cases, the combined power of exclusion was 0.6405 for 13 polymorphic SNPs and 0.6405 for 9 non-binary SNPs. Non-binary loci have a greater discrimination power and exclusion power per SNP.

  2. Optical energy gaps and photoluminescence peaks of BaGa{sub 2}S{sub 4}:Er{sup 3+} and BaGa{sub 2}Se{sub 4}:Er{sup 3+} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Choe, Sung-Hyu [Chosun University, Kwangju (Korea, Republic of); Jin, Moon-Seog [Dongshin University, Naju (Korea, Republic of); Kim, Wha-Tek [Chonnam National University, Kwangju (Korea, Republic of)

    2005-12-15

    BaGa{sub 2}S{sub 4}:Er{sup 3+} and BaGa{sub 2}Se{sub 4}:Er{sup 3+} single crystals were grown by using the chemical transport reaction method. The optical energy gaps of the BaGa{sub 2}S{sub 4}:Er{sup 3+} and the BaGa{sub 2}Se{sub 4}:Er{sup 3+} single crystals were found to be 4.045 eV and 3.073 eV, respectively, at 11 K. The temperature dependence of the optical energy gap was well fitted by the Varshni equation. Sharp emission peaks were observed in the photoluminescence spectra of the single crystals and assigned to radiation recombination between split Stark levels of the Er{sup 3+} ion.

  3. Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I

    NARCIS (Netherlands)

    Bogomolovas, J.; Fleming, J.R.; Anderson, B.R.; Williams, R.; Lange, S.; Simon, B.; Khan, M.M.; Rudolf, R.; Franke, B.; Bullard, B.; Rigden, D.J.; Granzier, H.; Labeit, S.; Mayans, O.

    2016-01-01

    Missense single-nucleotide polymorphisms (mSNPs) in titin are emerging as a main causative factor of heart failure. However, distinguishing between benign and disease-causing mSNPs is a substantial challenge. Here, we research the question of whether a single mSNP in a generic domain of titin can

  4. Finding the right coverage : The impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates

    NARCIS (Netherlands)

    Fountain, Emily D.; Pauli, Jonathan N.; Reid, Brendan N.; Palsboll, Per J.; Peery, M. Zachariah

    Restriction-enzyme-based sequencing methods enable the genotyping of thousands of single nucleotide polymorphism (SNP) loci in nonmodel organisms. However, in contrast to traditional genetic markers, genotyping error rates in SNPs derived from restriction-enzyme-based methods remain largely unknown.

  5. Computational Analysis of Single Nucleotide Polymorphisms Associated with Altered Drug Responsiveness in Type 2 Diabetes

    Directory of Open Access Journals (Sweden)

    Valerio Costa

    2016-06-01

    Full Text Available Type 2 diabetes (T2D is one of the most frequent mortality causes in western countries, with rapidly increasing prevalence. Anti-diabetic drugs are the first therapeutic approach, although many patients develop drug resistance. Most drug responsiveness variability can be explained by genetic causes. Inter-individual variability is principally due to single nucleotide polymorphisms, and differential drug responsiveness has been correlated to alteration in genes involved in drug metabolism (CYP2C9 or insulin signaling (IRS1, ABCC8, KCNJ11 and PPARG. However, most genome-wide association studies did not provide clues about the contribution of DNA variations to impaired drug responsiveness. Thus, characterizing T2D drug responsiveness variants is needed to guide clinicians toward tailored therapeutic approaches. Here, we extensively investigated polymorphisms associated with altered drug response in T2D, predicting their effects in silico. Combining different computational approaches, we focused on the expression pattern of genes correlated to drug resistance and inferred evolutionary conservation of polymorphic residues, computationally predicting the biochemical properties of polymorphic proteins. Using RNA-Sequencing followed by targeted validation, we identified and experimentally confirmed that two nucleotide variations in the CAPN10 gene—currently annotated as intronic—fall within two new transcripts in this locus. Additionally, we found that a Single Nucleotide Polymorphism (SNP, currently reported as intergenic, maps to the intron of a new transcript, harboring CAPN10 and GPR35 genes, which undergoes non-sense mediated decay. Finally, we analyzed variants that fall into non-coding regulatory regions of yet underestimated functional significance, predicting that some of them can potentially affect gene expression and/or post-transcriptional regulation of mRNAs affecting the splicing.

  6. Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene.

    OpenAIRE

    Richaud, F; Richaud, C; Ratet, P; Patte, J C

    1986-01-01

    In Escherichia coli, the first enzyme of the diaminopimelate and lysine pathway is dihydrodipicolinate synthetase, which is feedback-inhibited by lysine and encoded by the dapA gene. The location of the dapA gene on the bacterial chromosome has been determined accurately with respect to the neighboring purC and dapE genes. The complete nucleotide sequence and the transcriptional start of the dapA gene were determined. The results show that dapA consists of a single cistron encoding a 292-amin...

  7. Hydrogen sulfide (H{sub 2}S)/cystathionine γ-lyase (CSE) pathway contributes to the proliferation of hepatoma cells

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Yan; Ye, Shuang; Yuan, Dexiao; Zhang, Jianghong; Bai, Yang; Shao, Chunlin, E-mail: clshao@shmu.edu.cn

    2014-05-15

    Highlights: • Inhibition of H{sub 2}S/CSE pathway strongly stimulates cellular apoptosis. • Inhibition of H{sub 2}S/CSE pathway suppresses cell growth by blocking EGFR pathway. • H{sub 2}S/CSE pathway is critical for maintaining the proliferation of hepatoma cells. - Abstract: Hydrogen sulfide (H{sub 2}S)/cystathionine γ-lyase (CSE) pathway has been demonstrated to play vital roles in physiology and pathophysiology. However, its role in tumor cell proliferation remains largely unclear. Here we found that CSE over-expressed in hepatoma HepG2 and PLC/PRF/5 cells. Inhibition of endogenous H{sub 2}S/CSE pathway drastically decreased the proliferation of HepG2 and PLC/PRF/5 cells, and it also enhanced ROS production and mitochondrial disruption, pronounced DNA damage and increased apoptosis. Moreover, this increase of apoptosis was associated with the activation of p53 and p21 accompanied by a decreased ratio of Bcl-2/Bax and up-regulation of phosphorylated c-Jun N-terminal kinase (JNK) and caspase-3 activity. In addition, the negative regulation of cell proliferation by inhibition of H{sub 2}S/CSE system correlated with the blockage of cell mitogenic and survival signal transduction of epidermal growth factor receptor (EGFR) via down-regulating the extracellular-signal-regulated kinase 1/2 (ERK1/2) activation. These results demonstrate that H{sub 2}S/CSE and its downstream pathway contribute to the proliferation of hepatoma cells, and inhibition of this pathway strongly suppress the excessive growth of hepatoma cells by stimulating mitochondrial apoptosis and suppressing cell growth signal transduction.

  8. Alfredo Häberli ja Iittala : Senta / Piret Veigel

    Index Scriptorium Estoniae

    Veigel, Piret, 1961-

    2004-01-01

    Jaanuaris Pariisi messil Maison & Objet aasta disaineriks kuulutatud Alfredo Häberli esitles veebruaris Frankfurdi messil Ambiente oma neljandat ühisprojekti Soome Iittalaga: Senta-nimelisi valge, punase ja vahuveini klaase

  9. Heterojunction metal-oxide-metal Au-Fe{sub 3}O{sub 4}-Au single nanowire device for spintronics

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, K. M., E-mail: mrkongara@boisestate.edu; Punnoose, Alex; Hanna, Charles [Department of Physics, Boise State University, Boise, Idaho 83725 (United States); Padture, Nitin P. [School of Engineering, Brown University, Providence, Rhode Island 02912 (United States)

    2015-05-07

    In this report, we present the synthesis of heterojunction magnetite nanowires in alumina template and describe magnetic and electrical properties from a single nanowire device for spintronics applications. Heterojunction Au-Fe-Au nanowire arrays were electrodeposited in porous aluminum oxide templates, and an extensive and controlled heat treatment process converted Fe segment to nanocrystalline cubic magnetite phase with well-defined Au-Fe{sub 3}O{sub 4} interfaces as confirmed by the transmission electron microscopy. Magnetic measurements revealed Verwey transition shoulder around 120 K and a room temperature coercive field of 90 Oe. Current–voltage (I-V) characteristics of a single Au-Fe{sub 3}O{sub 4}-Au nanowire have exhibited Ohmic behavior. Anomalous positive magnetoresistance of about 0.5% is observed on a single nanowire, which is attributed to the high spin polarization in nanowire device with pure Fe{sub 3}O{sub 4} phase and nanocontact barrier. This work demonstrates the ability to preserve the pristine Fe{sub 3}O{sub 4} and well defined electrode contact metal (Au)–magnetite interface, which helps in attaining high spin polarized current.

  10. Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes

    International Nuclear Information System (INIS)

    Wang, Xuting; Tomso, Daniel J.; Liu Xuemei; Bell, Douglas A.

    2005-01-01

    Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes

  11. Effect of secondary structure on single nucleotide polymorphism detection with a porous microarray matrix; implications for probe selection

    NARCIS (Netherlands)

    Anthony, R. M.; Schuitema, A. R. J.; Chan, A. B.; Boender, P. J.; Klatser, P. R.; Oskam, L.

    2003-01-01

    Oligonucleotide arrays capable of detecting single nucleotide polymorphisms (SNPs) from amplified nucleic acid have many applications. The expected SNP is usually placed approximately in the center of the probe to ensure the maximum shift in Tm between complementary and SNP sequences. Unfortunately,

  12. An alternative membrane transport pathway for phosphate and adenine nucleotides in mitochondria and its possible function

    Science.gov (United States)

    Reynafarje, Baltazar; Lehninger, Albert L.

    1978-01-01

    This paper describes the properties and a possible biological role of a transport process across the inner membrane of rat liver mitochondria resulting in the exchange of ATP4- (out) for ADP3- (in) + 0.5 phosphate2- (in). This transmembrane exchange reaction, designated as the ATP-ADP-phosphate exchange, is specific for the ligands shown, electroneutral, insensitive to N-ethylmaleimide or mersalyl, inhibited by atractyloside, and appears to occur only in the direction as written. It is thus distinct from the well-known phosphate-hydroxide and phosphate-dicarboxylate exchange systems, which are inhibited by mersalyl, and from the ATP-ADP exchanger, which does not transport phosphate. During ATP hydrolysis by mitochondria, half of the phosphate formed from ATP passes from the matrix to the medium by the mersalyl-insensitive ATP-ADP-phosphate exchange and the other half by the well-known mersalyl-sensitive phosphate-hydroxide exchange. These and other considerations have led to a hypothesis for the pathway and stoichiometry of ATP-dependent reverse electron transport, characterized by a requirement of 1.33 molecules of ATP per pair of electrons reversed and by the utilization of a different membrane transport pathway for phosphate and adenine nucleotides than is taken in forward electron flow and oxidative phosphorylation. The possible occurrence of independent pathways for ATP-forming forward electron flow and ATP-consuming reverse electron flow is consonant with the fact that the opposing degradative and synthetic pathways in the central routes of cell metabolism generally have different pathways that are independently regulated. PMID:283393

  13. Important role of the nucleotide excision repair pathway in Mycobacterium smegmatis in conferring protection against commonly encountered DNA-damaging agents.

    Science.gov (United States)

    Kurthkoti, Krishna; Kumar, Pradeep; Jain, Ruchi; Varshney, Umesh

    2008-09-01

    Mycobacteria are an important group of human pathogens. Although the DNA repair mechanisms in mycobacteria are not well understood, these are vital for the pathogen's persistence in the host macrophages. In this study, we generated a null mutation in the uvrB gene of Mycobacterium smegmatis to allow us to compare the significance of the nucleotide excision repair (NER) pathway with two important base excision repair pathways, initiated by uracil DNA glycosylase (Ung) and formamidopyrimidine DNA glycosylase (Fpg or MutM), in an isogenic strain background. The strain deficient in NER was the most sensitive to commonly encountered DNA-damaging agents such as UV, low pH, reactive oxygen species, hypoxia, and was also sensitive to acidified nitrite. Taken together with previous observations on NER-deficient M. tuberculosis, these results suggest that NER is an important DNA repair pathway in mycobacteria.

  14. Impact of sodium on the secondary phases and current pathway in Cu{sub 2}(Zn,Sn)Se{sub 4} thin film solar cell

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yi-Cheng, E-mail: ielinyc@cc.ncue.edu.tw [Department of Mechatronics Engineering, National Changhua University of Education, Changhua, Taiwan (China); Lai, Chien-Mu [Department of Mechatronics Engineering, National Changhua University of Education, Changhua, Taiwan (China); Hsu, Hung-Ru [Green Energy & Environment Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan (China)

    2017-05-01

    In this study, we investigated the influence of Na content on secondary phases and current pathway in Cu{sub 2}(Zn,Sn)Se{sub 4} (CZTSe) thin film solar cells with the following structure: Ti/Mo:Na/Mo/CZTSe/CdS/i-ZnO/ZnO:Al/Al. The application of Na-doped Mo target as a source of sodium. Experimental results demonstrate that increasing the Na content leads to an increase in the quantity of secondary phase SnSe{sub 2} on the surface of the absorber layer; however, it did not appear to affect the secondary phases of Cu{sub 2}SnSe{sub 3} (CTSe) or ZnSe. Excessive quantities of Na were shown to have an adverse effect on device efficiency. Our results using conductive atomic force microscopy (C-AFM) revealed that an increase in the quantity of secondary phase SnSe{sub 2} can shift the current pathway on the surface of CZTSe from CZTSe grain boundaries (GBs) to the SnSe{sub 2} grains. The role of secondary phase SnSe{sub 2} of the CZTSe acted as a channel for the current flow, which results in high leakage current and low device efficiency. - Highlights: • Increasing the Na content leads to an increase in the quantity of secondary phase SnSe{sub 2}. • An increase of secondary phase SnSe{sub 2} can shift the current pathway from CZTSe grain boundaries to the SnSe{sub 2} grains. • The secondary phase SnSe{sub 2} acted as a channel for the current flow, which results in high leakage current.

  15. Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli.

    Science.gov (United States)

    Shimada, Tomohiro; Kori, Ayako; Ishihama, Akira

    2013-07-01

    Escherichia coli is able to utilize d-ribose as its sole carbon source. The genes for the transport and initial-step metabolism of d-ribose form a single rbsDACBK operon. RbsABC forms the ABC-type high-affinity d-ribose transporter, while RbsD and RbsK are involved in the conversion of d-ribose into d-ribose 5-phosphate. In the absence of inducer d-ribose, the ribose operon is repressed by a LacI-type transcription factor RbsR, which is encoded by a gene located downstream of this ribose operon. At present, the rbs operon is believed to be the only target of regulation by RbsR. After Genomic SELEX screening, however, we have identified that RbsR binds not only to the rbs promoter but also to the promoters of a set of genes involved in purine nucleotide metabolism. Northern blotting analysis indicated that RbsR represses the purHD operon for de novo synthesis of purine nucleotide but activates the add and udk genes involved in the salvage pathway of purine nucleotide synthesis. Taken together, we propose that RbsR is a global regulator for switch control between the de novo synthesis of purine nucleotides and its salvage pathway. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  16. Nucleotide excision repair in yeast

    NARCIS (Netherlands)

    Eijk, Patrick van

    2012-01-01

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

  17. Risk of estrogen receptor-positive and -negative breast cancer and single-nucleotide polymorphism 2q35-rs13387042

    DEFF Research Database (Denmark)

    Milne, Roger L; Benítez, Javier; Nevanlinna, Heli

    2009-01-01

    BACKGROUND: A recent genome-wide association study identified single-nucleotide polymorphism (SNP) 2q35-rs13387042 as a marker of susceptibility to estrogen receptor (ER)-positive breast cancer. We attempted to confirm this association using the Breast Cancer Association Consortium. METHODS: 2q35...

  18. DNA detection and single nucleotide mutation identification using SERS for molecular diagnostics and global health

    Science.gov (United States)

    Ngo, Hoan T.; Gandra, Naveen; Fales, Andrew M.; Taylor, Steve M.; Vo-Dinh, Tuan

    2017-02-01

    Nucleic acid-based molecular diagnostics at the point-of-care (POC) and in resource-limited settings is still a challenge. We present a sensitive yet simple DNA detection method with single nucleotide polymorphism (SNP) identification capability. The detection scheme involves sandwich hybridization of magnetic beads conjugated with capture probes, target sequences, and ultrabright surface-enhanced Raman Scattering (SERS) nanorattles conjugated with reporter probes. Upon hybridization, the sandwich probes are concentrated at the detection focus controlled by a magnetic system for SERS measurements. The ultrabright SERS nanorattles, consisting of a core and a shell with resonance Raman reporters loaded in the gap space between the core and the shell, serve as SERS tags for ultrasensitive signal detection. Specific DNA sequences of the malaria parasite Plasmodium falciparum and dengue virus 1 (DENV1) were used as the model marker system. Detection limit of approximately 100 attomoles was achieved. Single nucleotide polymorphism (SNP) discrimination of wild type malaria DNA and mutant malaria DNA, which confers resistance to artemisinin drugs, was also demonstrated. The results demonstrate the molecular diagnostic potential of the nanorattle-based method to both detect and genotype infectious pathogens. The method's simplicity makes it a suitable candidate for molecular diagnosis at the POC and in resource-limited settings.

  19. Single crystal structures of the new vanadates CuMgVO{sub 4} and AgMgVO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Ben Yahia, Hamdi, E-mail: Hyahia@qf.org.qa [Research Institute of Electrochemical Energy, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577 (Japan); Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, PO Box 5825, Doha (Qatar); Shikano, Masahiro, E-mail: shikano.masahiro@aist.go.jp [Research Institute of Electrochemical Energy, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577 (Japan); Essehli, Rachid; Belharouak, Ilias [Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, PO Box 5825, Doha (Qatar)

    2016-08-01

    The new compounds CuMgVO{sub 4} and AgMgVO{sub 4} have been synthesized by a solid state reaction route. Their crystal structures were determined from single-crystal X-ray diffraction data. CuMgVO{sub 4} crystallizes with Na{sub 2}CrO{sub 4}-type structure with space group Cmcm, a = 5.6932 (10), b = 8.7055 (15), c = 6.2789 (10) Å, V = 311.20 (9) Å{sup 3}, and Z = 4, whereas AgMgVO{sub 4} crystallizes in the maricite-type structure with space group Pnma, a = 9.4286 (14), b = 6.7465 (10), c = 5.3360 (8) Å, V = 339.42 (9) Å{sup 3}, and Z = 4. Both structures of CuMgVO{sub 4}, and AgMgVO{sub 4} contain MgO{sub 4} chains made up of edge-sharing MgO{sub 6} octahedra. In CuMgVO{sub 4} the MgO{sub 4} chains are interconnected through CuVO{sub 4} double chains made up of VO{sub 4} and CuO{sub 4} tetrahedra sharing corners and edges, however in AgMgVO{sub 4} the chains are interlinked by the VO{sub 4} and AgO{sub 4} tetrahedra sharing only corners. - Highlights: • We have been able to grow CuMgVO{sub 4} and AgMgVO{sub 4} single crystals. • We solved their crystal structures using single crystal data. • We compared the crystal structures of CuMgVO{sub 4} and AgMgVO{sub 4}.

  20. Different diffusion mechanisms of oxygen in ReBa{sub 2}Cu{sub 3}O{sub 7−x} (Re = Y, Ho) single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Vovk, R.V.; Boiko, Y.I.; Bogdanov, V.V.; Kamchatnaya, S.N.; Goulatis, I.L. [V. N. Karazin Kharkiv National University, 4 Svobody sq., 61077 Kharkiv (Ukraine); Chroneos, A. [Faculty of Engineering, Environment and Computing, Coventry University, Priory Street, Coventry CV1 5FB (United Kingdom); Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom)

    2017-05-15

    Highlights: • Single file diffusion mechanism of oxygen ions. • Ho modifies the diffusion mechanism in the oxygen sublattice. • Ho changes the efficient interaction of ions in CuO-planes. - Abstract: In the present study, the time dependencies of the resistivity of ReBa{sub 2}Cu{sub 3}O{sub 7−x} (Re=Y, Ho) single crystals with varying degree of deviation from oxygen stoichiometry was investigated. It was shown that the accelerated transport of oxygen ions in the initial stage of the process can be carried out along the one-dimensional non-stoichiometric vacancies’ accumulation by the single file diffusion mechanism. The final phase redistribution of oxygen ions in ReBa{sub 2}Cu{sub 3}O{sub 7−x} (Re = Y, Ho) is described by the classical mechanism of volume diffusion. The substitution of yttrium by holmium significantly affects the charge redistribution and changes the efficient interaction of ions in CuO-planes, thereby modifying the mass transfer diffusion mechanisms in the oxygen sublattice. Thus, a significant length change of the time intervals occurs, corresponding to the oxygen ions’ single file and volume diffusion mechanisms.

  1. Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene.

    Science.gov (United States)

    Richaud, F; Richaud, C; Ratet, P; Patte, J C

    1986-04-01

    In Escherichia coli, the first enzyme of the diaminopimelate and lysine pathway is dihydrodipicolinate synthetase, which is feedback-inhibited by lysine and encoded by the dapA gene. The location of the dapA gene on the bacterial chromosome has been determined accurately with respect to the neighboring purC and dapE genes. The complete nucleotide sequence and the transcriptional start of the dapA gene were determined. The results show that dapA consists of a single cistron encoding a 292-amino acid polypeptide of 31,372 daltons.

  2. Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene.

    Science.gov (United States)

    Richaud, F; Richaud, C; Ratet, P; Patte, J C

    1986-01-01

    In Escherichia coli, the first enzyme of the diaminopimelate and lysine pathway is dihydrodipicolinate synthetase, which is feedback-inhibited by lysine and encoded by the dapA gene. The location of the dapA gene on the bacterial chromosome has been determined accurately with respect to the neighboring purC and dapE genes. The complete nucleotide sequence and the transcriptional start of the dapA gene were determined. The results show that dapA consists of a single cistron encoding a 292-amino acid polypeptide of 31,372 daltons. Images PMID:3514578

  3. Reinvestigations of six unusual paternity cases by typing of autosomal single-nucleotide polymorphisms

    DEFF Research Database (Denmark)

    Børsting, Claus; Morling, Niels

    2012-01-01

    and published as case work examples in forensic journals. Here, the cases were reinvestigated by typing the samples for 49 autosomal single-nucleotide polymorphisms (SNPs) using the SNPforID multiplex assay. RESULTS: Three cases were solved by the SNP investigation without the need for any additional testing....... In two cases, the SNP results supported the conclusions based on STRs. In the last case, the SNP results spoke in favor of paternity, and the combined paternity index based on autosomal STRs and SNPs was 12.3 billion. Nevertheless, the alleged father was excluded by X-chromosome typing. CONCLUSION...

  4. Sub-megahertz linewidth single photon source

    Directory of Open Access Journals (Sweden)

    Markus Rambach

    2016-12-01

    Full Text Available We report 100% duty cycle generation of sub-MHz single photon pairs at the rubidium D1 line using cavity-enhanced spontaneous parametric downconversion. The temporal intensity cross correlation function exhibits a bandwidth of 666±16 kHz for the single photons, an order of magnitude below the natural linewidth of the target transition. A half-wave plate inside our cavity helps to achieve triple resonance between pump, signal, and idler photon, reducing the bandwidth and simplifying the locking scheme. Additionally, stabilisation of the cavity to the pump frequency enables the 100% duty cycle. The quantum nature of the source is confirmed by the idler-triggered second-order autocorrelation function at τ=0 to be gs,s(2(0= 0.016±0.002 for a heralding rate of 5 kHz. The generated photons are well-suited for storage in quantum memory schemes with sub-natural linewidths, such as gradient echo memories.

  5. Aging characteristics of 0.7Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-0.3PbTiO{sub 3} single crystals with different crystal orientations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xing [Changzhou University, School of Materials Science and Engineering, Jiangsu Collaborative Innovation Center of Photovoltaic Science and Engineering, Changzhou (China); Chinese Academy of Sciences, Key Laboratory of Inorganic Function Material and Device, Shanghai (China); Wu, Dun; Fang, Bijun [Changzhou University, School of Materials Science and Engineering, Jiangsu Collaborative Innovation Center of Photovoltaic Science and Engineering, Changzhou (China); Ding, Jianning [Changzhou University, School of Materials Science and Engineering, Jiangsu Collaborative Innovation Center of Photovoltaic Science and Engineering, Changzhou (China); Jiangsu University, School of Material Science and Engineering, Zhenjiang (China); Li, Xiaobing; Zhao, Xiangyong; Luo, Haosu [Chinese Academy of Sciences, Key Laboratory of Inorganic Function Material and Device, Shanghai (China); Ko, Jae-Hyeon [Hallym University, Department of Physics, Chuncheon (Korea, Republic of); Ahn, Chang Won [University of Ulsan, Department of Physics and EHSRC, Ulsan (Korea, Republic of)

    2015-06-15

    In this work, the time and temperature dependence of the piezoelectric and ferroelectric properties of the 0.7Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-0.3PbTiO{sub 3} (0.7PMN-0.3PT) single crystals were investigated in order to search for an effective method to improve their properties further. The piezoelectric properties of the [001]-, [110]- and [111]-oriented 0.7PMN-0.3PT single crystals exhibit excellent time stability during the 2-month room-temperature aging process. The re-poling process leads to the improvement of piezoelectric constant d{sub 33} for the [001]-, [110]- and [111]-oriented 0.7PMN-0.3PT single crystals, while the values of electromechanical coupling coefficient k{sub t} change little. During the thermal aging, the values of the measured d{sub 33}, calculated converse piezoelectric constant d{sub 33}{sup *}, maximum strain S{sub max}% and longitudinal electrostrictive coefficient Q of the [001]-, [110]- and [111]-oriented crystal plates increase gradually before the ferroelectric phase transition temperatures (T{sub FPT}, T{sub R-M}, T{sub R-O} and T{sub R-T}) and then decline continuously. The increase in these values before the T{sub FPT} is a result of the phase instability. In general, the [001]- and [110]-oriented 0.7PMN-0.3PT single crystals exhibit large piezoelectricity, excellent time stability and relatively high thermal stability between 20 and 80 C, which is favorable to the piezoelectric applications. (orig.)

  6. Efficient Oligo nucleotide mediated CRISPR-Cas9 Gene Editing in Aspergilli

    DEFF Research Database (Denmark)

    Nødvig, Christina Spuur; Hoof, Jakob Blæsbjerg; Kogle, Martin Engelhard

    2018-01-01

    CRISPR-Cas9 technologies are revolutionizing fungal gene editing. Here we show that survival of specific Cas9/sgRNA mediated DNA double strand breaks (DSBs) depends on the non-homologous end-joining, NHEJ, DNA repair pathway and we use this observation to develop a tool to assess protospacer....... niger, and in A. oryzae indicating that this type of repair may be wide spread in filamentous fungi. Importantly, we demonstrate that by using single-stranded oligo nucleotides for CRISPR-Cas9 mediated gene editing it is possible to introduce specific point mutations as well gene deletions...

  7. Single-crystal LiNi{sub 0.6}Co{sub 0.2}Mn{sub 0.2}O{sub 2} as high performance cathode materials for Li-ion batteries

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lei [School of Materials Science and Engineering, Beijing Institute of Technology, Beijing Key Laboratory of Environment Science and Engineering, Beijing 100081 (China); Wu, Borong, E-mail: wubr@bit.edu.cn [School of Materials Science and Engineering, Beijing Institute of Technology, Beijing Key Laboratory of Environment Science and Engineering, Beijing 100081 (China); Beijing Higher Institution Engineering Research Center of Power Battery and Chemical Energy Materials, Beijing 100081 (China); Collaborative Innovation Center of Electric Vehicles in Beijing, Beijing 100081 (China); Mu, Daobin, E-mail: mudb@bit.edu.cn [School of Materials Science and Engineering, Beijing Institute of Technology, Beijing Key Laboratory of Environment Science and Engineering, Beijing 100081 (China); Beijing Higher Institution Engineering Research Center of Power Battery and Chemical Energy Materials, Beijing 100081 (China); Liu, Xiaojiang [Institute of Electric Engineering, China Academy of Engineering Physics, Mianyang 621900 (China); Peng, Yiyuan [Key Laboratory of Small Fuctional Organic Molecule, Ministry of Education, Jiangxi Normal University, Nanchang 330022 (China); Xu, Hongliang; Liu, Qi; Gai, Liang [School of Materials Science and Engineering, Beijing Institute of Technology, Beijing Key Laboratory of Environment Science and Engineering, Beijing 100081 (China); Wu, Feng [School of Materials Science and Engineering, Beijing Institute of Technology, Beijing Key Laboratory of Environment Science and Engineering, Beijing 100081 (China); Beijing Higher Institution Engineering Research Center of Power Battery and Chemical Energy Materials, Beijing 100081 (China); Collaborative Innovation Center of Electric Vehicles in Beijing, Beijing 100081 (China)

    2016-07-25

    Single-crystal nickel-high materials (ST-LNCMO) LiNi{sub 0.6}Co{sub 0.2}Mn{sub 0.2}O{sub 2} have been synthesized using a versatile hydrothermal method. The as-prepared samples are characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), transmission electron microscope (TEM), and selected area electron diffraction (SAED). The results show that the sample annealed at an optimized temperature of 850 °C reveals uniform fine well-crystallized single-particles with diameters of ~800 nm. Electrochemical data demonstrate that the cell using this nickel-high material as the cathode exhibits excellent performance. The sample displays a high capacity of 183.7 mA h·g{sup −1} at 36 mA·g{sup −1} (0.2 C) and excellent cycling stability at different rates. It yields an initial discharge capacity of 153.6 mA h·g{sup −1} at a rate of 10C-rate and a voltage of 2.8 V – 4.3 V. The sample also has an outstanding rate capacity at a high cut-off voltage (4.6 V). This superior performance is attributed to the merits of the single-crystal structure, which may be beneficial to the transportation of the Li{sup +} ion along the grain. - Highlights: • A single-crystal LiNi{sub 0.6}Co{sub 0.2}Mn{sub 0.2}O{sub 2} is prepared by a hydrothermal method. • A high discharge capacity of 183.7 mA h·g{sup −1} at 0.2 C and good cycling stability. • It yields an initial discharge capacity of 153.6 mA h·g{sup −1} at 10 C-rate under 2.8 V–4.3 V. • Superior electrochemical performance may be obtained attributed to the single-crystal structure.

  8. Role of microRNA Pathway in Mental Retardation

    Science.gov (United States)

    Qurashi, Abrar; Chang, Shuang; Jin, Peng

    2007-01-01

    Deficits in cognitive functions lead to mental retardation (MR). Understanding the genetic basis of inherited MR has provided insights into the pathogenesis of MR. Fragile X syndrome is one of the most common forms of inherited MR, caused by the loss of functional Fragile X Mental Retardation Protein (FMRP). MicroRNAs (miRNAs) are endogenous, single-stranded RNAs between 18 and 25 nucleotides in length, which have been implicated in diversified biological pathways. Recent studies have linked the miRNA pathway to fragile X syndrome. Here we review the role of the miRNA pathway in fragile X syndrome and discuss its implication in MR in general. PMID:17982588

  9. Single Nucleotide Polymorphisms in Selected Apoptotic Genes and BPDE-Induced Apoptotic Capacity in Apparently Normal Primary Lymphocytes: A Genotype-Phenotype Correlation Analysis

    International Nuclear Information System (INIS)

    Hu, Z.; Li, Ch.; Chen, K.; Wang, L.E.; Sturgis, E.M.; Spitz, M.R.; Wei, Q.; Sturgis, E.M.

    2008-01-01

    Apoptotic capacity (AC) in primary lymphocytes may be a marker for cancer susceptibility, and functional single nucleotide polymorphisms (SNPs) in genes involved in apoptotic pathways may modulate cellular AC in response to DNA damage. To further examine the correlation between apoptotic genotypes and phenotype, we geno typed 14 published SNPs in 11 apoptosis-related genes (i.e., p53, Bcl-2, BAX, CASP9, DR4, Fas, FasL, CASP8, CASP10, CASP3, and CASP7) and assessed the AC in response to benzo[a]pyrene-7,8-9,10-diol epoxide (BPDE) in cultured primary lymphocytes from 172 cancer-free subjects. We found that among these 14 SNPs, R72P, intron 3 16-bp del/ins, and intron 6 G>A in , −938C>A in Bcl-2, and I522L in CASP10 were significant predictors of the BPDE-induced lymphocytic AC in single-locus analysis. In the combined analysis of the three variants, we found that the individuals with the diplotypes carrying 0-1 copy of the common R-del-G haplotype had higher AC values compared to other genotypes. Although the study size may not have the statistical power to detect the role of other SNPs in AC, our findings suggest that some SNPs in genes involved in the intrinsic apoptotic pathway may modulate lymphocytic AC in response to BPDE exposure in the general population. Larger studies are needed to validate these findings for further studying individual susceptibility to cancer and other apoptosis-related diseases

  10. Bulgarian Emergency Response System (BERS) in case of nuclear accident with exposure doses’estimation

    Energy Technology Data Exchange (ETDEWEB)

    Syrakov, M.; Prodanova, M.; Slavov, K.; Veleva, B.

    2015-07-01

    A PC-oriented Emergency Response System in case of nuclear accident (BERS) is developed and works operationally in the National Institute of Meteorology and Hydrology (NIMH). The creation and development of BERS was highly stimulated by the ETEX (European Tracer Experiment) project. BERS comprises two main parts - the operational and the accidental ones. The operational part, run automatically every 12 hours, prepares the input meteorological file used by both trajectory and dispersion models, runs the trajectory models, visualizes the results and uploads the maps of trajectories to a dedicated web-site. The accidental part is activated manually when a real radioactive releases occur or during emergency exercises. Its core is the Bulgarian dispersion models EMAP. Outputs are concentration, accumulated deposition and selected doses fields. In the paper, the BERS overall structure is described and examples of its products are presented. (Author)

  11. A Cross-Cancer Genetic Association Analysis of the DNA Repair and DNA Damage Signaling Pathways for Lung, Ovary, Prostate, Breast, and Colorectal Cancer.

    Science.gov (United States)

    Scarbrough, Peter M; Weber, Rachel Palmieri; Iversen, Edwin S; Brhane, Yonathan; Amos, Christopher I; Kraft, Peter; Hung, Rayjean J; Sellers, Thomas A; Witte, John S; Pharoah, Paul; Henderson, Brian E; Gruber, Stephen B; Hunter, David J; Garber, Judy E; Joshi, Amit D; McDonnell, Kevin; Easton, Doug F; Eeles, Ros; Kote-Jarai, Zsofia; Muir, Kenneth; Doherty, Jennifer A; Schildkraut, Joellen M

    2016-01-01

    DNA damage is an established mediator of carcinogenesis, although genome-wide association studies (GWAS) have identified few significant loci. This cross-cancer site, pooled analysis was performed to increase the power to detect common variants of DNA repair genes associated with cancer susceptibility. We conducted a cross-cancer analysis of 60,297 single nucleotide polymorphisms, at 229 DNA repair gene regions, using data from the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) Network. Our analysis included data from 32 GWAS and 48,734 controls and 51,537 cases across five cancer sites (breast, colon, lung, ovary, and prostate). Because of the unavailability of individual data, data were analyzed at the aggregate level. Meta-analysis was performed using the Association analysis for SubSETs (ASSET) software. To test for genetic associations that might escape individual variant testing due to small effect sizes, pathway analysis of eight DNA repair pathways was performed using hierarchical modeling. We identified three susceptibility DNA repair genes, RAD51B (P cancer risk in the base excision repair, nucleotide excision repair, mismatch repair, and homologous recombination pathways. Only three susceptibility loci were identified, which had all been previously reported. In contrast, hierarchical modeling identified several pleiotropic cancer risk associations in key DNA repair pathways. Results suggest that many common variants in DNA repair genes are likely associated with cancer susceptibility through small effect sizes that do not meet stringent significance testing criteria. ©2015 American Association for Cancer Research.

  12. Genetic study of two single nucleotide polymorphisms within corresponding microRNAs and susceptibility to tuberculosis in a Chinese Tibetan and Han population.

    Science.gov (United States)

    Li, Dongdong; Li, Dingdong; Wang, Tingting; Song, Xingbo; Qucuo, MeiLang; Yang, Bin; Zhang, Junlong; Wang, Jun; Ying, Binwu; Tao, Chuanmin; Wang, Lanlan

    2011-07-01

    MicroRNAs (miRNA) are thought to play important roles in the pathogenesis of diseases. Single nucleotide polymorphisms (SNPs) within miRNAs can change their characteristics via altering their target selection and/or expression, resulting in functional and/or phenotypic changes. We decided to investigate the genetic association with pulmonary tuberculosis with 2 nucleotide variations within corresponding microRNAs regulating the Toll-like receptor (TLR)-mediating signal pathway. MiRNAs potentially regulating the TLR-mediating signal pathway were predicted via bioinformatics. Finally, 2 SNPs, rs2910164 G>C and rs3746444 T>C within miR-146a and miR-499, were selected as candidates in accordance with some criteria. SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism and validated by sequencing to demonstrate their association with susceptibility to pulmonary tuberculosis (PTB) in 337 PTB cases and 738 healthy controls, including 318 Tibetan and 757 Han individuals. Bioinformatics databases were searched to support the association between miRNAs and PTB. There was no association between rs3746444 and PTB risk (p = 0.118) in the Han population, but subjects carrying the C allele exhibited decreased PTB risk (odds ratio [OR] = 0.403 [95% confidence interval (95% CI) 0.278-0.583]). However, there was an association between rs3746444 and PTB in the Tibetan population, and individuals carrying the C allele exhibited increased PTB risk (OR = 1.870 [95% CI 1.218-2.871]). A polymorphism (rs2910164 G>C) indicated an association with PTB risk in both Tibetan (p = 0.031) and Han (p = 0.000) populations. However, the role of the G allele of rs2910164, like the C allele in rs3746444, differed in the Tibetan (OR = 1.509, p tuberculosis with SNPs within the corresponding miRNAs potentially regulates the TLR signal pathway. It is interesting that both the G allele (rs2910164) and the C allele (rs3746444) play different roles in 2 populations

  13. Single-phase highly densified SrBi{sub 2}Ta{sub 2}O{sub 9} compacts produced by high-pressure sintering

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Altair Soria; Souza, Ricson Rocha de; Sousa, Vania Caldas de, E-mail: altair@if.ufrgs.br [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre (Brazil)

    2016-07-01

    Full text: The development of high-performance lead-free piezoelectric ceramics is an important scientific and technological challenge, as environmental and health issues have imposed restrictions to the use of lead zirconate titanates, the most employed material in ferroelectric devices [1]. Strontium bismuth tantalate (SBT),SrBi{sub 2}Ta{sub 2}O{sub 9}, is an interesting alternative ferroelectric material as its polarization can be modified at low voltages and it shows limited polarization switching fatigue. However, the production of highly densified single-phase bulk SBT by conventional sintering procedures is strongly compromised by stoichiometric changes due to bismuth loss. In this work, high-pressure sintering has been exploited as an alternative procedure to obtain SBT highly-densified single-phase compacts. Using toroidal-type high-pressure chambers, samples were produced by reaction sintering of BiTaO{sub 4} and SrCO{sub 3} powders, mixed in the stoichiometric ratio corresponding to SrBi{sub 2}Ta{sub 2}O{sub 9}, at pressures of 2.5 GPa and 7.7 GPa, and temperatures up to 1250°C, during 10 min. X-ray diffraction and scanning electron microscopy associated to energy-dispersive X-ray spectroscopy were used to follow the phase composition and the microstructure evolution as a function of the processing conditions. A single-phase SBT compact, with a relative density of 93% and a homogeneous microstructure, was produced by sintering at 2.5 GPa/900°C [2]. References: [1] K. Panda, J. Mater. Sci. 44, 5049-5062 (2009). [2] Ricson R.Souza, Rejane K. Kirchner, Jose R. Jurado, Altair S. Pereira, Vania C. Sousa. Journal of Solid State Chemistry 233, 259-268 (2016). (author)

  14. Solid electrolytes. Extremely fast charge carriers in garnet-type Li{sub 6}La{sub 3}ZrTaO{sub 12} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Stanje, Bernhard; Breuer, Stefan; Uitz, Marlena [Christian Doppler Laboratory for Lithium Batteries, and Institute for Chemistry and Technology of Materials, Graz University of Technology (NAWI Graz), Graz (Austria); DFG Research Unit ' ' Mobility of Lithium Ions in Solids' ' , Graz University of Technology, Graz (Austria); Rettenwander, Daniel; Redhammer, Guenther [Department Chemistry and Physics of Materials, University of Salzburg (Austria); Berendts, Stefan; Lerch, Martin [Technische Universitaet Berlin, Institut fuer Chemie (Germany); Uecker, Reinhard [Leibniz Institute for Crystal Growth (Forschungsverbund Berlin e.V.), Berlin (Germany); Hanzu, Ilie; Wilkening, Martin [Christian Doppler Laboratory for Lithium Batteries, and Institute for Chemistry and Technology of Materials, Graz University of Technology (NAWI Graz), Graz (Austria); DFG Research Unit ' ' Mobility of Lithium Ions in Solids' ' , Graz University of Technology, Graz (Austria); Alistore-ERI European Research Institute, Amiens (France)

    2017-12-15

    The development of all-solid-state electrochemical energy storage systems, such as lithium-ion batteries with solid electrolytes, requires stable, electronically insulating compounds with exceptionally high ionic conductivities. Considering ceramic oxides, garnet-type Li{sub 7}La{sub 3}Zr{sub 2}O{sub 12} and derivatives, see Zr-exchanged Li{sub 6}La{sub 3}ZrTaO{sub 12} (LLZTO), have attracted great attention due to its high Li{sup +} ionic conductivity of 10{sup -3} S cm{sup -1} at ambient temperature. Despite numerous studies focussing on conductivities of powder samples, only few use time-domain NMR methods to probe Li ion diffusion parameters in single crystals. Here we report on temperature-variable NMR relaxometry measurements using both laboratory and spin-lock techniques to probe Li jump rates covering a dynamic time window spanning several decades. Both techniques revealed a consistent picture of correlated Li ion jump diffusion in the single crystal; the data perfectly mirror a modified BPP-type relaxation response being based on a Lorentzian-shaped relaxation function. The rates measured could be parameterized with a single set of diffusion parameters. Results from NMR are completely in line with ion transport parameters derived from conductivity spectroscopy. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  15. Crystallographic and single-particle analyses of native- and nucleotide-bound forms of the cystic fibrosis transmembrane conductance regulator (CFTR) protein.

    Science.gov (United States)

    Awayn, N H; Rosenberg, M F; Kamis, A B; Aleksandrov, L A; Riordan, J R; Ford, R C

    2005-11-01

    Cystic fibrosis, one of the major human inherited diseases, is caused by defects in the CFTR (cystic fibrosis transmembrane conductance regulator), a cell-membrane protein. CFTR acts as a chloride channel which can be opened by ATP. Low-resolution structural studies of purified recombinant human CFTR are described in the present paper. Localization of the C-terminal decahistidine tag in CFTR was achieved by Ni2+-nitriloacetate nanogold labelling, followed by electron microscopy and single-particle analysis. The presence of the gold label appears to improve the single-particle-alignment procedure. Projection structures of CFTR from two-dimensional crystals analysed by electron crystallography displayed two alternative conformational states in the presence of nucleotide and nanogold, but only one form of the protein was observed in the quiescent (nucleotide-free) state.

  16. Genotypic distribution of single nucleotide polymorphisms in oral cancer: global scene.

    Science.gov (United States)

    Multani, Shaleen; Saranath, Dhananjaya

    2016-11-01

    Globocan 2012 reports the global oral cancer incidence of 300,373 new oral cancer cases annually, contributing to 2.1 % of the world cancer burden. The major well-established risk factors for oral cancer include tobacco, betel/areca nut, alcohol and high-risk oncogenic human papilloma virus (HPV) 16/18. However, only 5-10 % of individuals with high-risk lifestyle develop oral cancer. Thus, genomic variants in individuals represented as single nucleotide polymorphisms (SNPs) influence susceptibility to oral cancer. With a view to understanding the role of genomic variants in oral cancer, we reviewed SNPs in case-control studies with a minimum of 100 cases and 100 controls. PubMed and HuGE navigator search engines were used to obtain data published from 1990 to 2015, which identified 67 articles investigating the role of SNPs in oral cancer. Single publications reported 93 SNPs in 55 genes, with 34 SNPs associated with a risk of oral cancer. Meta-analysis of data in multiple studies defined nine SNPs associated with a risk of oral cancer. The genes were associated with critical functions deregulated in cancers, including cell proliferation, immune function, inflammation, transcription, DNA repair and xenobiotic metabolism.

  17. Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma

    International Nuclear Information System (INIS)

    Tan, Min-Han; Furge, Kyle A; Kort, Eric; Giraud, Sophie; Ferlicot, Sophie; Vielh, Philippe; Amsellem-Ouazana, Delphine; Debré, Bernard; Flam, Thierry; Thiounn, Nicolas; Zerbib, Marc; Wong, Chin Fong; Benoît, Gérard; Droupy, Stéphane; Molinié, Vincent; Vieillefond, Annick; Tan, Puay Hoon; Richard, Stéphane; Teh, Bin Tean; Tan, Hwei Ling; Yang, Ximing J; Ditlev, Jonathon; Matsuda, Daisuke; Khoo, Sok Kean; Sugimura, Jun; Fujioka, Tomoaki

    2010-01-01

    Chromophobe renal cell carcinoma (chRCC) and renal oncocytoma are two distinct but closely related entities with strong morphologic and genetic similarities. While chRCC is a malignant tumor, oncocytoma is usually regarded as a benign entity. The overlapping characteristics are best explained by a common cellular origin, and the biologic differences between chRCC and oncocytoma are therefore of considerable interest in terms of carcinogenesis, diagnosis and clinical management. Previous studies have been relatively limited in terms of examining the differences between oncocytoma and chromophobe RCC. Gene expression profiling using the Affymetrix HGU133Plus2 platform was applied on chRCC (n = 15) and oncocytoma specimens (n = 15). Supervised analysis was applied to identify a discriminatory gene signature, as well as differentially expressed genes. High throughput single-nucleotide polymorphism (SNP) genotyping was performed on independent samples (n = 14) using Affymetrix GeneChip Mapping 100 K arrays to assess correlation between expression and gene copy number. Immunohistochemical validation was performed in an independent set of tumors. A novel 14 probe-set signature was developed to classify the tumors internally with 93% accuracy, and this was successfully validated on an external data-set with 94% accuracy. Pathway analysis highlighted clinically relevant dysregulated pathways of c-erbB2 and mammalian target of rapamycin (mTOR) signaling in chRCC, but no significant differences in p-AKT or extracellular HER2 expression was identified on immunohistochemistry. Loss of chromosome 1p, reflected in both cytogenetic and expression analysis, is common to both entities, implying this may be an early event in histogenesis. Multiple regional areas of cytogenetic alterations and corresponding expression biases differentiating the two entities were identified. Parafibromin, aquaporin 6, and synaptogyrin 3 were novel immunohistochemical markers effectively discriminating

  18. Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma

    Directory of Open Access Journals (Sweden)

    Thiounn Nicolas

    2010-05-01

    Full Text Available Abstract Background Chromophobe renal cell carcinoma (chRCC and renal oncocytoma are two distinct but closely related entities with strong morphologic and genetic similarities. While chRCC is a malignant tumor, oncocytoma is usually regarded as a benign entity. The overlapping characteristics are best explained by a common cellular origin, and the biologic differences between chRCC and oncocytoma are therefore of considerable interest in terms of carcinogenesis, diagnosis and clinical management. Previous studies have been relatively limited in terms of examining the differences between oncocytoma and chromophobe RCC. Methods Gene expression profiling using the Affymetrix HGU133Plus2 platform was applied on chRCC (n = 15 and oncocytoma specimens (n = 15. Supervised analysis was applied to identify a discriminatory gene signature, as well as differentially expressed genes. High throughput single-nucleotide polymorphism (SNP genotyping was performed on independent samples (n = 14 using Affymetrix GeneChip Mapping 100 K arrays to assess correlation between expression and gene copy number. Immunohistochemical validation was performed in an independent set of tumors. Results A novel 14 probe-set signature was developed to classify the tumors internally with 93% accuracy, and this was successfully validated on an external data-set with 94% accuracy. Pathway analysis highlighted clinically relevant dysregulated pathways of c-erbB2 and mammalian target of rapamycin (mTOR signaling in chRCC, but no significant differences in p-AKT or extracellular HER2 expression was identified on immunohistochemistry. Loss of chromosome 1p, reflected in both cytogenetic and expression analysis, is common to both entities, implying this may be an early event in histogenesis. Multiple regional areas of cytogenetic alterations and corresponding expression biases differentiating the two entities were identified. Parafibromin, aquaporin 6, and synaptogyrin 3 were novel

  19. Temperature dependent tunneling study of CaFe{sub 1.96}Ni{sub 0.04}As{sub 2} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Anirban, E-mail: adatta@iitk.ac.in; Gupta, Anjan K. [Department of Physics, IIT Kanpur, Kanpur-208 016 (India); Thamizhavel, A. [Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai-400 005 (India)

    2014-04-24

    We report on temperature dependent scanning tunneling microscopy and spectroscopy studies on CaFe{sub 1.96}Ni{sub 0.04}As{sub 2} single crystals in 5.4 – 19.7 K temperature range across the normal metal - superconductor transition temperature, T{sub C} = 14K. The in-situ cleaved crystals show reasonably flat surface with signatures of atomic resolution. The tunnel spectra show significant spatial inhomogeneity below T{sub C}, which reduces significantly as the temperature goes above the T{sub C}. We discuss these results in terms of an inhomogeneous electronic phase that may exist due to the vicinity of this composition to the quantum critical point.

  20. Temperature-induced spin reorientation and magnetization jump of rare-earth orthoferrite Ho{sub 0.5}Pr{sub 0.5}FeO{sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Guohua; Zhao, Weiyao; Cao, Yiming; Kang, Baojuan [Department of Physics, and International Center of Quantum and Molecular Structures, Shanghai University, Shanghai 200444 (China); Zhang, Jincang [Department of Physics, and International Center of Quantum and Molecular Structures, Shanghai University, Shanghai 200444 (China); Materials Genome Institute, Shanghai University, Shanghai 200444 (China); Shanghai Key Laboratory of High Temperature Superconductors, Shanghai University, Shanghai 200444 (China); Ren, Wei, E-mail: renwei@shu.edu.cn [Department of Physics, and International Center of Quantum and Molecular Structures, Shanghai University, Shanghai 200444 (China); Materials Genome Institute, Shanghai University, Shanghai 200444 (China); Shanghai Key Laboratory of High Temperature Superconductors, Shanghai University, Shanghai 200444 (China); Cao, Shixun, E-mail: sxcao@shu.edu.cn [Department of Physics, and International Center of Quantum and Molecular Structures, Shanghai University, Shanghai 200444 (China); Materials Genome Institute, Shanghai University, Shanghai 200444 (China); Shanghai Key Laboratory of High Temperature Superconductors, Shanghai University, Shanghai 200444 (China)

    2016-07-25

    We report temperature-induced spin reorientation and magnetization jump effects in the rare earth (RE) orthoferrite Ho{sub 0.5}Pr{sub 0.5}FeO{sub 3} single crystal. The single crystal of about 6 mm in diameter and 50 mm in length was successfully grown by optical floating zone method. Both X-ray diffraction and Laue photograph confirmed the homogeneity and high quality of the crystal. Magnetic properties of Ho{sub 0.5}Pr{sub 0.5}FeO{sub 3} single crystal are studied over a wide temperature range from 2 to 300 K. Spin reorientation transition from Γ{sub 2} to Γ{sub 4} phase is observed in the temperature range of 75–90 K. At lower temperature, the Ho{sub 0.5}Pr{sub 0.5}FeO{sub 3} shows an abrupt jump of magnetization along the a-axis, which occurs only in the field-cooling process, and is sensitive to external applied magnetic field. By analyzing the jump temperature and magnitude of the magnetization, we conclude that it is caused by the spin reversal of the rare earth ions. The isothermal magnetization versus field hysteresis loop measurements along a axis explain the spin configuration variation from 3 K to 60 K. - Highlights: • Ho{sub 0.5}Pr{sub 0.5}FeO{sub 3} single crystal was grown by optical floating zone method. • It shows an abrupt jump of magnetization along a axis at low temperature. • The jump height and temperature is sensitive to external applied magnetic field. • It is attributed to the spin reversal of the rare earth ions.

  1. No association between a common single nucleotide polymorphism, rs4141463, in the MACROD2 gene and autism spectrum disorder.

    NARCIS (Netherlands)

    Curran, S.; Bolton, P.; Rozsnyai, K.; Chiocchetti, A.; Klauck, S.M.; Duketis, E.; Poustka, F.; Schlitt, S.; Freitag, C.M.; Lee, I. van der; Muglia, P.; Poot, M.; Staal, W.G.; Jonge, M.V. de; Ophoff, R.A.; Lewis, C.; Skuse, D.; Mandy, W.; Vassos, E.; Fossdal, R.; Magnusson, P.; Hreidarsson, S.; Saemundsen, E.; Stefansson, H.; Stefansson, K.; Collier, D.

    2011-01-01

    The Autism Genome Project (AGP) Consortium recently reported genome-wide significant association between autism and an intronic single nucleotide polymorphism marker, rs4141463, within the MACROD2 gene. In the present study we attempted to replicate this finding using an independent case-control

  2. Pathway-based analyses.

    Science.gov (United States)

    Kent, Jack W

    2016-02-03

    New technologies for acquisition of genomic data, while offering unprecedented opportunities for genetic discovery, also impose severe burdens of interpretation and penalties for multiple testing. The Pathway-based Analyses Group of the Genetic Analysis Workshop 19 (GAW19) sought reduction of multiple-testing burden through various approaches to aggregation of highdimensional data in pathways informed by prior biological knowledge. Experimental methods testedincluded the use of "synthetic pathways" (random sets of genes) to estimate power and false-positive error rate of methods applied to simulated data; data reduction via independent components analysis, single-nucleotide polymorphism (SNP)-SNP interaction, and use of gene sets to estimate genetic similarity; and general assessment of the efficacy of prior biological knowledge to reduce the dimensionality of complex genomic data. The work of this group explored several promising approaches to managing high-dimensional data, with the caveat that these methods are necessarily constrained by the quality of external bioinformatic annotation.

  3. Single nucleotide polymorphism discrimination with and without an ethidium bromide intercalator

    International Nuclear Information System (INIS)

    Fenati, Renzo A.; Connolly, Ashley R.; Ellis, Amanda V.

    2017-01-01

    Single nucleotide polymorphism (SNP) genotyping is an important aspect in understanding genetic variations. Here, we discriminate SNPs using toe-hold mediated displacement reactions. The biological target is an 80 nucleotide long double-stranded–DNA from the mtDNA HV1 region, associated with maternal ancestry. This target has been specially designed with a pendant toehold and a cationic fluorophore, ATTO 647N, as a reporter, produced in a polymerase chain reaction. Rates of reaction for the toehold-polymerase chain reaction products (TPPs) with their corresponding complementary displacing sequences, labelled with a Black Hole Quencher 1, followed the order TPP–Cytosine > TPP–Thymine > TPP–Adenine ≥ TPP–Guanine. Non-complementary rates were the slowest with mismatches involving cytosine. These reactions, operating in a static/or contact mode, gave averaged readouts between SNPs within 15 min (with 80–90% quenching), compared to 25–30 min in previous studies involving fluorescence resonance energy transfer. Addition of an intercalating agent, ethidium bromide, retarded the rate of reaction in which cytosine was involved, presumably through stabilization of the base pairing, which resulted in markedly improved discrimination of cytosine containing SNPs. - Highlights: • Fluorophores and DNA intercalators effect the rate of toehold-mediated strand displacement. • Ethidium bromide had a destabilizing effect on mismatches that contained cytosine. • A cationic fluorophore and Black Hole Quencher 1 strand displacement system was 2–3 times faster than a FRET system. • This enabled SNP detection using toehold-mediated strand displacement in 15 min.

  4. Single nucleotide polymorphism discrimination with and without an ethidium bromide intercalator

    Energy Technology Data Exchange (ETDEWEB)

    Fenati, Renzo A.; Connolly, Ashley R. [Flinders Centre for Nanoscale Science and Technology, Flinders University, Sturt Road, Bedford Park, Adelaide, South Australia 5042 (Australia); Ellis, Amanda V., E-mail: amanda.ellis@flinders.edu.au [Flinders Centre for Nanoscale Science and Technology, Flinders University, Sturt Road, Bedford Park, Adelaide, South Australia 5042 (Australia); Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010 (Australia)

    2017-02-15

    Single nucleotide polymorphism (SNP) genotyping is an important aspect in understanding genetic variations. Here, we discriminate SNPs using toe-hold mediated displacement reactions. The biological target is an 80 nucleotide long double-stranded–DNA from the mtDNA HV1 region, associated with maternal ancestry. This target has been specially designed with a pendant toehold and a cationic fluorophore, ATTO 647N, as a reporter, produced in a polymerase chain reaction. Rates of reaction for the toehold-polymerase chain reaction products (TPPs) with their corresponding complementary displacing sequences, labelled with a Black Hole Quencher 1, followed the order TPP–Cytosine > TPP–Thymine > TPP–Adenine ≥ TPP–Guanine. Non-complementary rates were the slowest with mismatches involving cytosine. These reactions, operating in a static/or contact mode, gave averaged readouts between SNPs within 15 min (with 80–90% quenching), compared to 25–30 min in previous studies involving fluorescence resonance energy transfer. Addition of an intercalating agent, ethidium bromide, retarded the rate of reaction in which cytosine was involved, presumably through stabilization of the base pairing, which resulted in markedly improved discrimination of cytosine containing SNPs. - Highlights: • Fluorophores and DNA intercalators effect the rate of toehold-mediated strand displacement. • Ethidium bromide had a destabilizing effect on mismatches that contained cytosine. • A cationic fluorophore and Black Hole Quencher 1 strand displacement system was 2–3 times faster than a FRET system. • This enabled SNP detection using toehold-mediated strand displacement in 15 min.

  5. Guardians of the mycobacterial genome: A review on DNA repair systems in Mycobacterium tuberculosis.

    Science.gov (United States)

    Singh, Amandeep

    2017-12-01

    The genomic integrity of Mycobacterium tuberculosis is continuously threatened by the harsh survival conditions inside host macrophages, due to immune and antibiotic stresses. Faithful genome maintenance and repair must be accomplished under stress for the bacillus to survive in the host, necessitating a robust DNA repair system. The importance of DNA repair systems in pathogenesis is well established. Previous examination of the M. tuberculosis genome revealed homologues of almost all the major DNA repair systems, i.e. nucleotide excision repair (NER), base excision repair (BER), homologous recombination (HR) and non-homologous end joining (NHEJ). However, recent developments in the field have pointed to the presence of novel proteins and pathways in mycobacteria. Homologues of archeal mismatch repair proteins were recently reported in mycobacteria, a pathway previously thought to be absent. RecBCD, the major nuclease-helicase enzymes involved in HR in E. coli, were implicated in the single-strand annealing (SSA) pathway. Novel roles of archeo-eukaryotic primase (AEP) polymerases, previously thought to be exclusive to NHEJ, have been reported in BER. Many new proteins with a probable role in DNA repair have also been discovered. It is now realized that the DNA repair systems in M. tuberculosis are highly evolved and have redundant backup mechanisms to mend the damage. This review is an attempt to summarize our current understanding of the DNA repair systems in M. tuberculosis.

  6. Crystal growth and scintillation properties of Er-doped Lu{sub 3}Al{sub 5}O{sub 12} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Sugiyama, Makoto, E-mail: makoto.sugiyama@imr.tohoku.ac.jp [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577 (Japan); Fujimoto, Yutaka [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577 (Japan); Yanagida, Takayuki [New Industry Creation Hatchery Center (NICHe), Tohoku University, 6-6-10 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 (Japan); Totsuka, Daisuke [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577 (Japan); Nihon Kessho Kogaku Co. Ltd., 810-5 Nobe-cho Tatebayashi Gunma (Japan); Kurosawa, Shunsuke; Futami, Yoshisuke; Yokota, Yuui; Chani, Valery [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577 (Japan); Yoshikawa, Akira [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577 (Japan); New Industry Creation Hatchery Center (NICHe), Tohoku University, 6-6-10 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579 (Japan)

    2012-02-01

    Er-doped Lu{sub 3}Al{sub 5}O{sub 12} (Er:LuAG) single crystalline scintillators with different Er concentrations of 0.1, 0.5, 1, and 3% were grown by the micro-pulling-down ({mu}-PD) method. The grown crystals were composed of single-phase material, as demonstrated by powder X-ray diffraction (XRD). The radioluminescence spectra measured under {sup 241}Am {alpha}-ray excitation indicated host emission at approximately 350 nm and Er{sup 3+} 4f-4f emissions. According to the pulse height spectra recorded under {gamma}-ray irradiation, the 0.5% Er:LuAG exhibited the highest peak channel among the samples. The {gamma}-ray excited decay time profiles were well fitted by the two-component exponential approximation (0.8 {mu}s and 6-10 {mu}s).

  7. Dopa-responsive dystonia: functional analysis of single nucleotide substitutions within the 5' untranslated GCH1 region.

    Directory of Open Access Journals (Sweden)

    Ioanna A Armata

    Full Text Available BACKGROUND: Mutations in the GCH1 gene are associated with childhood onset, dopa-responsive dystonia (DRD. Correct diagnosis of DRD is crucial, given the potential for complete recovery once treated with L-dopa. The majority of DRD associated mutations lie within the coding region of the GCH1 gene, but three additional single nucleotide sequence substitutions have been reported within the 5' untranslated (5'UTR region of the mRNA. The biologic significance of these 5'UTR GCH1 sequence substitutions has not been analyzed. METHODOLOGY/PRINCIPAL FINDINGS: Luciferase reporter assays, quantitative real time PCR and RNA decay assays, combined with bioinformatics, revealed a pathogenic 5'UTR GCH1 substitution. The +142C>T single nucleotide 5'UTR substitution that segregates with affected status in DRD patients, substantially attenuates translation without altering RNA expression levels or stability. The +142C>T substitution disrupts translation most likely by creating an upstream initiation start codon (uAUG and an upstream open reading frame (uORF. CONCLUSIONS/SIGNIFICANCE: This is the first GCH1 regulatory substitution reported to act at a post-transcriptional level, increasing the list of genetic diseases caused by abnormal translation and reaffirming the importance of investigating potential regulatory substitutions in genetic diseases.

  8. Bulgarian Emergency Response System (BERS) in case of nuclear accident with exposure doses estimation

    Energy Technology Data Exchange (ETDEWEB)

    Syrakov, D.; Prodanova, M.; Slavov, K.; Veleva, B.

    2015-07-01

    A PC-oriented Emergency Response System in case of nuclear accident (BERS) is developed and works operationally in the National Institute of Meteorology and Hydrology (NIMH). The creation and development of BERS was highly stimulated by the ETEX (European Tracer Experiment) project. BERS comprises two main parts - the operational and the accidental ones. The operational part, run automatically every 12 hours, prepares the input meteorological file used by both trajectory and dispersion models, runs the trajectory models, visualizes the results and uploads the maps of trajectories to a dedicated web-site. The accidental part is activated manually when a real radioactive releases occur or during emergency exercises. Its core is the Bulgarian dispersion models EMAP. Outputs are concentration, accumulated deposition and selected doses fields. In the paper, the BERS overall structure is described and examples of its products are presented. Key words: nuclear accident, emergency response, early warning system, air dispersion models, radioactive exposure dose. (Author)

  9. ACRT technique for the single crystal growth of the heavy fermion compound YbRh{sub 2}Si{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Witt, Sebastian; Kliemt, Kristin; Butzke, Constantin; Krellner, Cornelius [Goethe University Frankfurt, 60438 Frankfurt am Main (Germany)

    2016-07-01

    In the heavy fermion compound YbRh{sub 2}Si{sub 2} the antiferromagnetic ordering below 70 mK close to a quantum critical point is well-studied. Beneath the magnetic ordering a new phase transition was found recently at 2 mK. It is necessary to prepare large and high-quality single crystals for studying the nature of this new phase transition. Besides the optimization of the single crystal growth it is important to investigate single crystals with different isotopes at this phase transition. Here, we report the crystal growth of YbRh{sub 2}Si{sub 2} with the accelerated crucible rotation technique (ACRT). ACRT shows for other compounds, e.g. YAG (yttrium aluminum garnet, Y{sub 3}Al{sub 5}O{sub 12}), that this technique can reduce flux impurities and enhance the yield of larger crystals. We also report the attempt to receive metallic isotopes of ytterbium with metallothermic reduction. Crystals with different isotopes of silicon and ytterbium can be used for NMR measurements to investigate the underlying phenomena of quantum criticality in more detail.

  10. The single-nucleotide polymorphism 309 in the MDM2 gene contributes to the Li-Fraumeni syndrome and related phenotypes

    NARCIS (Netherlands)

    Ruijs, Mariëlle W. G.; Schmidt, Marjanka K.; Nevanlinna, Heli; Tommiska, Johanna; Aittomäki, Kristiina; Pruntel, Roelof; Verhoef, Senno; van 't Veer, L. J.

    2007-01-01

    Li-Fraumeni syndrome (LFS) is an autosomal-dominant cancer predisposition syndrome of which the majority is caused by TP53 germline mutations and is characterised by different tumour types occurring at relatively young age. Recently, it was shown that a single-nucleotide polymorphism (SNP) in the

  11. Functional single nucleotide polymorphisms within the cyclin-dependent kinase inhibitor 2A/2B region affect pancreatic cancer risk

    Czech Academy of Sciences Publication Activity Database

    Campa, D.; Pastore, M.; Gentiluomo, M.; Talar-Wojnarowska, R.; Kupcinskas, J.; Malecka-Panas, E.; Neoptolemos, J. P.; Niesen, W.; Vodička, Pavel; Delle Fave, G.; Bueno-de-Mesquita, H. B.; Gazouli, M.; Pacetti, P.; Di Leo, M.; Ito, H.; Klüter, H.; Souček, P.; Corbo, V.; Yamao, K.; Hosono, S.; Kaaks, R.; Vashist, Y.; Gioffreda, D.; Strobel, O.; Shimizu, Y.; Dijk, F.; Andriulli, A.; Ivanauskas, A.; Bugert, P.; Tavano, F.; Vodičková, L.; Zambon, C.F.; Lovecek, M.; Landi, S.; Key, T. J.; Boggi, U.; Pezzilli, R.; Jamroziak, K.; Mohelníková-Duchoňová, B.; Mambrini, A.; Bambi, F.; Busch, O.; Pazienza, V.; Valente, R.; Theodoropoulos, G.E.; Hackert, T.; Capurso, G.; Cavestro, G.M.; Pasquali, C.; Basso, D.; Sperti, C.; Matsuo, K.; Büchler, M.; Khaw, K. T.; Izbicki, J.; Costello, E.; Katzke, V.; Michalski, Ch.; Stepien, A.; Rizzato, C.; Canzian, F.

    2016-01-01

    Roč. 7, č. 35 (2016), s. 57011-57020 ISSN 1949-2553 R&D Projects: GA ČR GAP301/12/1734 Institutional support: RVO:68378041 Keywords : pancreatic cancer * CDKN2A * single nucleotide polymorphisms Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.168, year: 2016

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

    Directory of Open Access Journals (Sweden)

    Nathaniel Holcomb

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

  13. Temperature-dependent Raman spectra and electrical properties of 0.69Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-0.31PbTiO{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Bijun [Changzhou University, School of Materials Science and Engineering, Jiangsu Collaborative Innovation Center of Photovolatic Science and Engineering, Changzhou (China); Liu, Xing [Changzhou University, School of Materials Science and Engineering, Jiangsu Collaborative Innovation Center of Photovolatic Science and Engineering, Changzhou (China); Chinese Academy of Sciences, Key Laboratory of Inorganic Function Material and Device, Shanghai (China); Li, Xiaobing; Zhao, Xiangyong; Luo, Haosu [Chinese Academy of Sciences, Key Laboratory of Inorganic Function Material and Device, Shanghai (China); Ding, Jianning [Changzhou University, School of Materials Science and Engineering, Jiangsu Collaborative Innovation Center of Photovolatic Science and Engineering, Changzhou (China); Jiangsu University, School of Material Science and Engineering, Zhenjiang (China)

    2016-09-15

    The temperature-dependent Raman spectra and electrical properties of the 0.69Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-0.31PbTiO{sub 3} (0.69PMN-0.31PT) single crystals were investigated. Based on the group theory, the poled 0.69PMN-0.31PT single crystals belong to the monoclinic crystal system, which was confirmed by the room-temperature Raman spectra. The 0.69PMN-0.31PT single crystals experience successive structural phase transitions, i.e., a monoclinic-tetragonal (FE{sub M}-FE{sub T}) phase transition at T{sub M-T} and a tetragonal-cubic (FE{sub T}-P{sub C}) phase transition at T{sub m} determined by the dielectric measurement. Due to the enhancement of long-range order, their FE{sub M}-FE{sub T} phase transition becomes more obvious after the poling process. The wavenumbers and line widths of the 271, 502, 575, 795 cm{sup -1} Raman modes, and the intensity ratios of I{sub 271cm}{sup {sub -}{sub 1}}/I{sub 795cm}{sup {sub -}{sub 1}} and I{sub 502cm}{sup {sub -}{sub 1}}/I{sub 575cm}{sup {sub -}{sub 1}} exhibit obvious anomalies around T{sub M-T} and T{sub m}, which are closely related to the FE{sub M}-FE{sub T} and FE{sub T}-P{sub C} phase transitions. The temperature and electric field (E)-induced phase transitions are observed in the unipolar strain-E (S-E) curves. The converse piezoelectric constant (d{sub 33}), maximum strain value (S{sub max}%) and longitudinal electrostrictive coefficient (Q) increase considerably around the ferroelectric phase transition temperature T{sub M-T}. (orig.)

  14. Optical and magnetic spectroscopy of rare-earth-doped yttrium aluminium borate (YAl sub 3 (BO sub 3) sub 4) single crystals

    CERN Document Server

    Watterich, A; Borowiec, M T; Zayarnyuk, T; Szymczak, H; Beregi, E; Kovács, L G

    2003-01-01

    For Ce sup 3 sup + , Er sup 3 sup + and Yb sup 3 sup + ions, electron paramagnetic resonance (EPR) spectra typical for S' = 1/2 ions are measured for YAl sub 3 (BO sub 3) sub 4 (YAB) single crystal. The spectra show axial symmetry indicating that all three dopants replace Y sup 3 sup + at the given dopant concentration. Corresponding g-tilde - and hyperfine A-tilde -tensors are determined. The EPR linewidth of Ce broadens with increasing temperature due to an Orbach relaxation process. Fitting the curve with an exponential, the energy difference is found to be equal to 270 +- 16 cm sup - sup 1. The optical absorption and excitation spectra of Ce in YAB single crystal measured at 300 K are similar to those found for polycrystalline materials. High-resolution polarized emission from the lowest excited to the sup 2 F sub 5 sub / sub 2 ground state, measured at 4.2 K, indicates a splitting of the ground state into three levels. The second level is located 277 +- 18 cm sup - sup 1 above the first one, in excellent...

  15. Structural study of intermediate phase in layered perovskite SrBi sub 2 Ta sub 2 O sub 9 single crystal

    CERN Document Server

    Onodera, A; Yamashita, H

    2003-01-01

    The crystal structure of an intermediate phase of Bi-layered ferroelectric SrBi sub 2 Ta sub 2 O sub 9 single crystals was studied by means of X-ray diffraction. An analysis of the extinction rules and X-ray intensities demonstrated that the crystal structure is orthorhombic with space group A2 sub 1 am in the ferroelectric phase and Amam in the intermediate phase; this conclusion is in good agreement with the findings of previous powder neutron diffraction studies.

  16. Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population

    DEFF Research Database (Denmark)

    Fabbri, Elena; Caniglia, R.; Mucci, Nadia

    2012-01-01

    Single nucleotide polymorphisms (SNPs) which represent the most widespread source of sequence variation in genomes, are becoming a routine application in several fields such as forensics, ecology and conservation genetics. Their use, requiring short amplifications, may allow a more efficient geno....... We evaluated the cost, laboratory effort and reliability of these different markers and discuss the possible future use of VeraCode, SNPlex and Fluidigm EP1 system in wild population monitoring....

  17. Growth and microtopographic study of CuInSe{sub 2} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Chauhan, Sanjaysinh M.; Chaki, Sunil, E-mail: sunilchaki@yahoo.co.in; Deshpande, M. P. [Department of Physics, Sardar Patel University, Vallabh Vidyanagar, Gujarat - 388120 (India); Tailor, J. P. [Applied Physics Department, S.V.N.I.T., Surat, Gujarat - 395007 (India)

    2016-05-23

    The CuInSe{sub 2} single crystals were grown by chemical vapour transport (CVT) technique using iodine as transporting agent. The elemental composition of the as-grown CuInSe{sub 2} single crystals was determined by energy dispersive analysis of X-ray (EDAX). The unit cell crystal structure and lattice parameters were determined by X-ray diffraction (XRD) technique. The surface microtopographic study of the as-grown CuInSe{sub 2} single crystals surfaces were done to study the defects, growth mechanism, etc. of the CVT grown crystals.

  18. DFT investigation of NH{sub 3}, PH{sub 3}, and AsH{sub 3} adsorptions on Sc-, Ti-, V-, and Cr-doped single-walled carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Buasaeng, Prayut; Rakrai, Wandee [Computational Chemistry Center for Nanotechnology and Department of Chemistry, Faculty of Science and Technology, Rajabhat Maha Sarakham University, Maha Sarakham, 44000 (Thailand); Wanno, Banchob [Center of Excellence for Innovation in Chemistry and Supramolecular Chemistry Research Unit, Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, 44150 (Thailand); Tabtimsai, Chanukorn, E-mail: tabtimsai.c@gmail.com [Computational Chemistry Center for Nanotechnology and Department of Chemistry, Faculty of Science and Technology, Rajabhat Maha Sarakham University, Maha Sarakham, 44000 (Thailand)

    2017-04-01

    Highlights: • Transition metal-doped single wall carbon nanotubes and their adsorption with NH{sub 3}, PH{sub 3} and AsH{sub 3} molecules were investigated using a DFT method. • Adsorptions of NH{sub 3}, PH{sub 3} and AsH{sub 3} molecules on pristine single wall carbon nanotubeswere improved by transition metal doping. • Structural and electronic properties of single wall carbon nanotubes were significantly changed by transition metal doping and gas adsorptions. - Abstract: The adsorption properties of ammonia (NH{sub 3}), phosphine (PH{sub 3}), and arsine (AsH{sub 3}) on pristine and transition metal- (TM = Sc, Ti, V, and Cr) doped (5,5) armchair single-walled carbon nanotubes (SWCNTs) were theoretically investigated. The geometric and electronic properties and adsorption abilities for the most stable configuration of NH{sub 3}, PH{sub 3}, and AsH{sub 3} adsorptions on pristine and TM-doped SWCNTs were calculated. It was found that the binding abilities of TMs to the SWCNT were in the order: Cr > V > Sc > Ti. However, the adsorption energy showed that the pristine SWCNT weakly adsorbed gas molecules and its electronic properties were also insensitive to gas molecules. By replacing a C atom with TM atoms, all doping can significantly enhance the adsorption energy of gas/SWCNT complexes and their adsorption ability was in the same order: NH{sub 3} > PH{sub 3} > AsH{sub 3}. A remarkable increase in adsorption energy and charge transfer of these systems was expected to induce significant changes in the electrical conductivity of the TM-doped SWCNTs. This work revealed that the sensitivity of SWCNT-based chemical gas adsorptions and sensors can be greatly improved by introducing an appropriate TM dopant. Accordingly, TM-doped SWCNTs are more suitable for gas molecule adsorptions and detections than the pristine SWCNT.

  19. Analysis Of Impact Of Various Parameters On BER Performance For IEEE 802.11b

    Directory of Open Access Journals (Sweden)

    Nilesh B. Kalani

    2015-08-01

    Full Text Available Abstract This paper discusses about IEEE 802.11b simulation model implemented using LabVIEW software and its analyses for impact on bit error rate BER for different parameters as channel type channel number data transmission rate and packet size. Audio file is being transmitted processed and analyzed using the model for various parameters. This paper gives analysis of BER verses ESN0 for various parameter like data rate packet size and communication channel for the IEEE 802.11b simulation model generated using LabVIEW. It is proved that BER can be optimized by tweaking different parameters of wireless communication system.

  20. A single crystal study of RE{sub 14}Co{sub 3}In{sub 3} (RE = Y, Tb, Dy, Ho, Er)

    Energy Technology Data Exchange (ETDEWEB)

    Zaremba, V.I.; Kalychak, Y.M.; Dzevenko, M.V. [Inorganic Chemistry Dept., Ivan Franko National Univ. of Lviv (Ukraine); Rodewald, U.Ch.; Heying, B.; Poettgen, R. [Inst. fuer Anorganische und Analytische Chemie, Westfaelische Wilhelms-Univ. Muenster (Germany)

    2006-01-01

    The rare earth-cobalt-indides RE{sub 14}Co{sub 3}In{sub 3} (RE = Y, Tb, Dy, Ho, Er) were prepared in polycrystalline form from the elements by arc-melting. Small single crystals were grown through a special annealing sequence. The compounds were investigated on the basis of X-ray powder and single crystal data: Lu{sub 14}Co{sub 2}In{sub 3} (Gd{sub 14}Co{sub 3}In{sub 2.7}) type, P4{sub 2}/nmc, Z = 4, a = 959.0(1), c = 2319.1(5) pm, wR2 = 0.055, 2289 F{sup 2} values, 65 variables for Y{sub 13.90}Co{sub 2.99}In{sub 3.02}, a = 953.8(1), c = 2315.8(5) pm, wR2 = 0.108, 2357 F{sup 2} values, 65 variables for Tb{sub 13.92}Co{sub 3.01}In{sub 2.92}, a = 949.24(3), c = 2296.5(1) pm, wR2 = 0.129, 2518 F{sup 2} values, 65 variables for Dy{sub 13.90}Co{sub 2.97}In{sub 2.95}, a = 946.3(1), c = 2289.0(5) pm, wR2 = 0.099, 2297 F{sup 2} values, 64 variables for Ho{sub 14}Co{sub 2.80}In{sub 2.89}, and a = 941.0(1), c = 2274.2(5) pm, wR2 = 0.140, 2450 F{sup 2} values, 65 variables for Er{sub 13.83}Co{sub 2.88}In{sub 3.10}. All RE{sub 14}Co{sub 3}In{sub 3} indides show a small degree of In/Co mixing (between 7 and 16% Co) on the 4c In1 site and defects on the 8g Co1 positions (between 84 and 95% Co). Except for the holmium compound, the RE{sub 14}Co{sub 3}In{sub 3} intermetallics also reveal RE/In mixing on the 4c RE1 sites, leading to the refined compositions. The seven crystallographically independent RE sites have between 9 and 10 nearest RE neighbors. The RE{sub 14}Co{sub 3}In{sub 3} structures consist of a complex intergrowth of rare earth based polyhedra. Both cobalt sites have a distorted trigonal-prismatic rare earth coordination. An interesting feature is the In2-In2 dumb-bell with an In2-In2 distance of 300 pm (for Ho{sub 14}Co{sub 2.80}In{sub 2.89}). The crystal chemistry of the RE{sub 14}Co{sub 3}In{sub 3} indides is discussed. (orig.)

  1. Crystal growth and mechanical hardness of In{sub 2}Se{sub 2.7}Sb{sub 0.3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Patel, Piyush, E-mail: piyush-patel130@yahoo.com; Vyas, S. M., E-mail: s-m-vyas-gu@hotmail.com; Patel, Vimal; Pavagadhi, Himanshu [Department of Physics, School of Science, Gujarat University, Ahmedabad, Gujarat, India-380009 (India); Solanki, Mitesh [panditdindayal Petroleum University, Gandhinagar. Gujarat (India); Jani, Maunik P. [BITS Edu Campus, Varnama, Vadodara, Gujarat (India)

    2015-08-28

    The III-VI compound semiconductors is important for the fabrication of ionizing radiation detectors, solid-state electrodes, and photosensitive heterostructures, solar cell and ionic batteries. In this paper, In{sub 2}Se{sub 2.7} Sb{sub 0.3} single crystals were grown by the Bridgman method with temperature gradient of 60 °C/cm and the growth velocity 0.5cm/hr. The as-grown crystals were examined under the optical microscope for surface study, a various growth features observed on top free surface of the single crystal which is predominant of layers growth mechanism. The lattice parameters of as-grown crystal was determined by the XRD analysis. A Vickers’ projection microscope were used for the study of microhardness on the as-cleaved, cold-worked and annealed samples of the crystals, the results were discussed, and reported in detail.

  2. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis.

    Science.gov (United States)

    Pisithkul, Tippapha; Jacobson, Tyler B; O'Brien, Thomas J; Stevenson, David M; Amador-Noguez, Daniel

    2015-09-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using (13)C-labeled sugars and [(15)N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. Copyright © 2015, Pisithkul et al.

  3. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis

    Science.gov (United States)

    Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.; Stevenson, David M.

    2015-01-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID:26070680

  4. High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification

    Directory of Open Access Journals (Sweden)

    Sun Zhenyu

    2001-08-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the foundation of powerful complex trait and pharmacogenomic analyses. The availability of large SNP databases, however, has emphasized a need for inexpensive SNP genotyping methods of commensurate simplicity, robustness, and scalability. We describe a solution-based, microtiter plate method for SNP genotyping of human genomic DNA. The method is based upon allele discrimination by ligation of open circle probes followed by rolling circle amplification of the signal using fluorescent primers. Only the probe with a 3' base complementary to the SNP is circularized by ligation. Results SNP scoring by ligation was optimized to a 100,000 fold discrimination against probe mismatched to the SNP. The assay was used to genotype 10 SNPs from a set of 192 genomic DNA samples in a high-throughput format. Assay directly from genomic DNA eliminates the need to preamplify the target as done for many other genotyping methods. The sensitivity of the assay was demonstrated by genotyping from 1 ng of genomic DNA. We demonstrate that the assay can detect a single molecule of the circularized probe. Conclusions Compatibility with homogeneous formats and the ability to assay small amounts of genomic DNA meets the exacting requirements of automated, high-throughput SNP scoring.

  5. Single-Nucleotide Polymorphism-Microarray Ploidy Analysis of Paraffin-Embedded Products of Conception in Recurrent Pregnancy Loss Evaluations.

    Science.gov (United States)

    Maslow, Bat-Sheva L; Budinetz, Tara; Sueldo, Carolina; Anspach, Erica; Engmann, Lawrence; Benadiva, Claudio; Nulsen, John C

    2015-07-01

    To compare the analysis of chromosome number from paraffin-embedded products of conception using single-nucleotide polymorphism (SNP) microarray with the recommended screening for the evaluation of couples presenting with recurrent pregnancy loss who do not have previous fetal cytogenetic data. We performed a retrospective cohort study including all women who presented for a new evaluation of recurrent pregnancy loss over a 2-year period (January 1, 2012, to December 31, 2013). All participants had at least two documented first-trimester losses and both the recommended screening tests and SNP microarray performed on at least one paraffin-embedded products of conception sample. Single-nucleotide polymorphism microarray identifies all 24 chromosomes (22 autosomes, X, and Y). Forty-two women with a total of 178 losses were included in the study. Paraffin-embedded products of conception from 62 losses were sent for SNP microarray. Single-nucleotide polymorphism microarray successfully diagnosed fetal chromosome number in 71% (44/62) of samples, of which 43% (19/44) were euploid and 57% (25/44) were noneuploid. Seven of 42 (17%) participants had abnormalities on recurrent pregnancy loss screening. The per-person detection rate for a cause of pregnancy loss was significantly higher in the SNP microarray (0.50; 95% confidence interval [CI] 0.36-0.64) compared with recurrent pregnancy loss evaluation (0.17; 95% CI 0.08-0.31) (P=.002). Participants with one or more euploid loss identified on paraffin-embedded products of conception were significantly more likely to have an abnormality on recurrent pregnancy loss screening than those with only noneuploid results (P=.028). The significance remained when controlling for age, number of losses, number of samples, and total pregnancies. These results suggest that SNP microarray testing of paraffin-embedded products of conception is a valuable tool for the evaluation of recurrent pregnancy loss in patients without prior fetal

  6. Impact of IL28B-Related Single Nucleotide Polymorphisms on Liver Histopathology in Chronic Hepatitis C Genotype 2 and 3

    DEFF Research Database (Denmark)

    Rembeck, Karolina; Alsiö, Asa; Christensen, Peer Brehm

    2012-01-01

    Recently, several genome-wide association studies have revealed that single nucleotide polymorphisms (SNPs) in proximity to IL28B predict spontaneous clearance of HCV infection as well as outcome following peginterferon and ribavirin therapy among HCV genotype 1 infected patients. The present stu...

  7. Evolution pathways for the formation of Nano-Cu{sub 2}ZnSnSe{sub 4} absorber materials via elemental sources and isophorondiamine chelation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, P.Y. [Institute of Microelectronics and Department of Electrical Engineering, Advanced Optoelectronic Technology Center, Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan 701, Taiwan (China); Shei, S.C., E-mail: scshei@mail.nutn.edu.tw [Department of Electrical Engineering, National University of Tainan, Tainan 70005, Taiwan (China); Chang, S.J. [Institute of Microelectronics and Department of Electrical Engineering, Advanced Optoelectronic Technology Center, Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan 701, Taiwan (China)

    2013-10-15

    Highlights: •We carry out the CZTSe nanocrystals in the isophorondiamine solution •We demonstrate the reaction from binary and ternary into quaternary nanocrystals. •We characterize the CZTSe nanocrystals with a stannite structure. -- Abstract: This paper reports the preparation of Cu{sub 2}ZnSnSe{sub 4} (CZTSe) nanocrystals via a method under nitrogen atmosphere at a temperature of 235 °C using elemental copper, zinc, tin, and Se powders as precursors, and isophorondiamine (IPDA) as a coordinating solvent. We investigated the influence of reaction time on the crystal structure, shape, particle size, optical properties, and composition of the nanocrystals. We also carried out a systematic study of the growth and evolution pathways of quaternary CZTSe nanocrystals in the IPDA solution. The reaction began with the formation of binary and ternary crystals, which subsequently transformed into Cu{sub 2}ZnSnSe{sub 4} nanocrystals. These binary and ternary compounds dissolved during the course of the reaction to produce the molecular precursor used in the formation of monophasic Cu{sub 2}ZnSnSe{sub 4} nanocrystals. Experimental results indicate that the phase changes in CZTSe nanocrystals are time-dependent. Spherical CZTSe nanocrystals with diameters in the range of 20–30 nm were obtained at 20 h. Characterization using X-ray diffraction (XRD) confirmed the as-synthesized CZTSe as single-phase quaternary nanocrystals with a stannite structure. The band gap energy of the as-synthesized CZTSe nanocrystals is 1.6 eV. The proposed process of synthesizing CZTSe nanocrystals is applicable to the production of inexpensive thin film solar cells using a relatively simple, low cost, and convenient coordinating solvent route.

  8. Nanoscale spatial non-homogeneity of 3D in {delta}{sub {pi}} Mg{sub 0.9}Al{sub 0.1}B{sub 2} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Giubileo, F. [CNR-INFM Laboratorio Regionale SUPERMAT e Dipartimento di Fisica ' E.R. Caianiello' , Universita degli Studi di Salerno, via Salvador Allende, 84081 Baronissi (Italy)], E-mail: giubileo@sa.infn.it; Bobba, F.; Scarfato, A. [CNR-INFM Laboratorio Regionale SUPERMAT e Dipartimento di Fisica ' E.R. Caianiello' , Universita degli Studi di Salerno, via Salvador Allende, 84081 Baronissi (Italy); Roditchev, D. [Institut des Nanosciences de Paris, INSP, Universite P. et M.Curie Paris 6, CNRS, UMR 75-88, Paris (France); Zhigadlo, N.; Karpinski, J. [Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich (Switzerland); Cucolo, A.M. [CNR-INFM Laboratorio Regionale SUPERMAT e Dipartimento di Fisica ' E.R. Caianiello' , Universita degli Studi di Salerno, via Salvador Allende, 84081 Baronissi (Italy)

    2007-09-01

    We have performed I(V) and dI/dV(V) measurements on high quality Mg{sub 0.9}Al{sub 0.1}B{sub 2} single crystals by means of a variable temperature scanning tunneling spectroscopy (STS) working in magnetic field up to 7 T. c-axis tunneling showed a single gap, probing the three-dimensional Dp that appeared highly non-homogeneous in its spatial distribution on nanometer scale, with an amplitude between 1.5 meV and 2.3 meV. Temperature and magnetic field dependence of the conductance spectra were studied in S-I-N configuration as well as in S-I-S configuration, after pushing the Pt/Ir tip in the sample to capture a superconducting grain at the very apex of the tip. For the largest energy gap (2.3 meV), we found H{sub c2} {approx} 3 T, i.e., a 25% raising with respect to what observed in the pure crystal.

  9. Structural study of quasi-one-dimensional vanadium pyroxene LiVSi{sub 2}O{sub 6} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Ishii, Yuto [Department of Physics, Hokkaido University, Sapporo 060-0810 (Japan); Matsushita, Yoshitaka [National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044 (Japan); Oda, Migaku; Yoshida, Hiroyuki [Department of Physics, Hokkaido University, Sapporo 060-0810 (Japan)

    2017-02-15

    Single crystals of quasi-one-dimensional vanadium pyroxene LiVSi{sub 2}O{sub 6} were synthesized and the crystal structures at 293 K and 113 K were studied using X-ray diffraction experiments. We found a structural phase transition from the room-temperature crystal structure with space group C2/c to a low-temperature structure with space group P2{sub 1}/c, resulting from a rotational displacement of SiO{sub 4} tetrahedra. The temperature dependence of magnetic susceptibility shows a broad maximum around 116 K, suggesting an opening of the Haldane gap expected for one-dimensional antiferromagnets with S=1. However, an antiferromagnetic long-range order was developed below 24 K, probably caused by a weak inter-chain magnetic coupling in the compound. - Graphical abstract: Low temperature crystal structure of LiVSi{sub 2}O{sub 6} and an orbital arrangement within the V-O zig-zag chain along the c-axis. - Highlights: • A low temperature structure of LiVSi{sub 2}O{sub 6} was determined by single crystal X-ray diffraction measurements. • The origin of the structural transition is a rotational displacement of SiO{sub 4} tetrahedra. • The uniform orbital overlap in the V-O zigzag chain makes the system a quasi one-dimensional antiferromagnet.

  10. Single crystal growth and low-temperature properties of Er{sub 3}Al{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Suttner, Christian; Benka, Georg; Bauer, Andreas; Pfleiderer, Christian [Physik Department, Technische Universitaet Muenchen, D-85748 Garching (Germany)

    2016-07-01

    In recent years, topologically non-trivial spin whirls in condensed matter systems attracted great scientific interest. Lattices of these objects, so-called magnetic skyrmion lattices, were mainly observed in Dzyaloshinskii-Moriya driven chiral magnets with the non-centrosymmetric cubic space group P2{sub 1}3. Similar spin textures, however, may in principle also arise in a large number of further compounds. We report single-crystal growth of Er{sub 3}Al{sub 2} crystallizing in the tetragonal space group P4{sub 2}/mnm by means of optical float zoning under UHV-compatible conditions. We determined the magnetic phase diagram for fields applied along different crystallographic directions using magnetization, ac susceptibility, and specific heat measurements. Several phase pockets are observed below the Neel temperature T{sub N} = 27 K, consistent with earlier reports.

  11. Intake of Total and Subgroups of Fat Minimally Affect the Associations between Selected Single Nucleotide Polymorphisms in the PPARγ Pathway and Changes in Anthropometry among European Adults from Cohorts of the DiOGenes Study

    DEFF Research Database (Denmark)

    Larsen, Sofus C; Ängquist, Lars; Østergaard, Jane N

    2016-01-01

    nucleotide polymorphisms (SNPs) within 4 genes in the PPARγ pathway are associated with the OR of being a BW gainer or with annual changes in anthropometry and whether intake of total fat, monounsaturated fat, polyunsaturated fat, or saturated fat has a modifying effect on these associations. METHODS: A case......-noncase study included 11,048 men and women from cohorts in the European Diet, Obesity and Genes study; 5552 were cases, defined as individuals with the greatest BW gain during follow-up, and 6548 were randomly selected, including 5496 noncases. We selected 4 genes [CCAAT/enhancer binding protein β (CEBPB...

  12. Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

    Science.gov (United States)

    Kondo, Jiro; Westhof, Eric

    2011-10-01

    Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

  13. Nachrichtenberichterstattung über Terrorismus. Eine Analyse der TV-Nachrichten über die Terroranschläge in Kenia 2002

    Directory of Open Access Journals (Sweden)

    Nicole Haußecker

    2007-04-01

    Full Text Available Nach der starken Kritik der Medienberichterstattung über Terrorismus, besonders nach dem 11.09.2001, werden die theoretischen Hintergründe ausgewählter Kritikpunkte betrachtet und ein weiteres terroristisches Ereignis, die Anschläge in Kenia am 28.11.2002, inhaltsanalytisch untersucht. Ziel dabei ist es, Aussagen bezüglich inhaltlicher und formaler Merkmale der Fernseh-berichterstattung über ein terroristisches Ereignis zu treffen. Deshalb liegt der Fokus auf den folgenden drei Forschungsfragen: 1. Welche Nachrichtenfaktoren spielen für die Selektion und Intensität der Berichterstattung über das terroristische Ereignis eine Rolle? 2. Wird mit Emotionalisierung gearbeitet? 3. Liegen negative Stereotype und/oder Feindbilder bezüglich der islamischen und arabischen Welt vor? Die Ergebnisse der Untersuchung zeigen erwartete Tendenzen sowohl die Merkmale der Terrorismusberichterstattung als auch die Senderkonvergenzen und -divergenzen im dualen System betreffend. Der Nachrichtenwert eines terroristischen Ereignisses ist anfänglich sehr hoch, jedoch verliert das Ereignis ab dem dritten Tag aufgrund diverser Nachrichtenfaktoren deutlich an Beachtung in der Berichterstattung. Das Vorkommen emotionalisierender Mittel wird empirisch bestätigt. Nicht nur emotionale Sprache und Sprechweise, sondern vor allem Formen der expliziten Emotionalisierung sind vertreten. Damit wird die Vermutung bekräftigt, dass die Medien die mit den terroristischen Ereignissen verbundene beängstigende Stimmung senderabhängig unterschiedlich stark aufgreifen. Ein direkter islamischer Feindbildaufbau ist in der Berichterstattung nicht zu verzeichnen. Allerdings liegen latente negative Bewertungstendenzen sowie negative Stereotype bezüglich der arabischen und islamischen Welt vor, die das seit dem 11.09.2001 negativ geprägte Bild festigen. Die meist narrativ inszenierte Fixierung auf Bin Laden und al Qaida erfolgt oberflächlich und vernachlässigt m

  14. Grossforschung in neuen Dimensionen : Denker unserer Zeit über die aktuelle Elementarteilchenphysik am CERN

    CERN Document Server

    Blanchard, Philippe; Kommer, Christoph; ZiF-Konferenz 2013; CERN : Large-scale Research in New Dimension

    2015-01-01

    Der 4. Juli 2012 stellt ein historisches Datum für das Europäische Kernforschungszentrum CERN in Genf dar: die Verkündung der Entdeckung des letzten, vorhergesagten, noch fehlenden und lange gesuchten Elementarteilchens, des Higgs-Bosons. Ein Jahr später kommen im Rahmen der Konferenz des Zentrums für interdisziplinäre Forschung (ZiF) in Bielefeld eine Vielzahl der mit dem Großprojekt am CERN verbundenen Wissenschaftler zusammen, um nicht nur über die Entdeckung des Teilchens, sondern vor allem über die Realisierung und Bedeutung eines derart ungeheuren Unterfangens für solch ein wissenschaftliches Großprojekt zu berichten. Der Generaldirektor des CERN, Prof. Dr. Rolf-Dieter Heuer, liefert in seinem Eröffnungsvortrag die Grundlage für die Diskussion der vielerlei Aspekte, die dabei ins Spiel kommen. So finden sich im vorliegenden Band zum einen Berichte über die Großforschung selbst: von der Entdeckung des Higgs-Teilchens über die Erforschung des Quark-Gluon-Plasmas und die Bedeutung von Th...

  15. Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk

    DEFF Research Database (Denmark)

    Goode, Ellen L; Fridley, Brooke L; Vierkant, Robert A

    2009-01-01

    Polymorphisms in genes critical to cell cycle control are outstanding candidates for association with ovarian cancer risk; numerous genes have been interrogated by multiple research groups using differing tagging single-nucleotide polymorphism (SNP) sets. To maximize information gleaned from......, and rs3212891; CDK2 rs2069391, rs2069414, and rs17528736; and CCNE1 rs3218036. These results exemplify the utility of imputation in candidate gene studies and lend evidence to a role of cell cycle genes in ovarian cancer etiology, suggest a reduced set of SNPs to target in additional cases and controls....

  16. The research reactor BER II at the Helmholtz-Center Berlin

    Energy Technology Data Exchange (ETDEWEB)

    Krohn, Herbert [Helmholtz-Zentrum Berlin (HZB), Berlin (Germany)

    2012-10-15

    For basic and application-oriented research assignments the Helmholtz-Center Berlin (Helmholtz Zentrum Berlin - HZB) runs a research reactor that operates as a source of neutron beams for a wide range of scientific investigations. At the end of the 1980{sup th} the BER II was completed renewed and fitted with new experimental facilities. The BER II is a light water cooled and moderated swimming pool type reactor to be operated at 10 MW thermal power. Six neutron guides deliver cold neutrons from the cold moderator cell to a neutron guide hall adjacent to the experiment hall. With its 24 experimental stations, experimenters at HZB have practically all neutron scattering or neutron radiography techniques at their disposal. (orig.)

  17. The research reactor BER II at the Helmholtz-Center Berlin

    International Nuclear Information System (INIS)

    Krohn, Herbert

    2012-01-01

    For basic and application-oriented research assignments the Helmholtz-Center Berlin (Helmholtz Zentrum Berlin - HZB) runs a research reactor that operates as a source of neutron beams for a wide range of scientific investigations. At the end of the 1980 th the BER II was completed renewed and fitted with new experimental facilities. The BER II is a light water cooled and moderated swimming pool type reactor to be operated at 10 MW thermal power. Six neutron guides deliver cold neutrons from the cold moderator cell to a neutron guide hall adjacent to the experiment hall. With its 24 experimental stations, experimenters at HZB have practically all neutron scattering or neutron radiography techniques at their disposal. (orig.)

  18. Amplitude Noise Suppression and Orthogonal Multiplexing Using Injection-Locked Single-Mode VCSEL

    DEFF Research Database (Denmark)

    Lyubopytov, Vladimir; von Lerber, Tuomo; Lassas, Matti

    2017-01-01

    We experimentally demonstrate BER reduction and orthogonal modulation using an injection locked single-mode VCSEL. It allows us suppressing an amplitude noise of optical signal and/or double the capacity of an information channel.......We experimentally demonstrate BER reduction and orthogonal modulation using an injection locked single-mode VCSEL. It allows us suppressing an amplitude noise of optical signal and/or double the capacity of an information channel....

  19. A New Closed Form Approximation for BER for Optical Wireless Systems in Weak Atmospheric Turbulence

    Science.gov (United States)

    Kaushik, Rahul; Khandelwal, Vineet; Jain, R. C.

    2018-04-01

    Weak atmospheric turbulence condition in an optical wireless communication (OWC) is captured by log-normal distribution. The analytical evaluation of average bit error rate (BER) of an OWC system under weak turbulence is intractable as it involves the statistical averaging of Gaussian Q-function over log-normal distribution. In this paper, a simple closed form approximation for BER of OWC system under weak turbulence is given. Computation of BER for various modulation schemes is carried out using proposed expression. The results obtained using proposed expression compare favorably with those obtained using Gauss-Hermite quadrature approximation and Monte Carlo Simulations.

  20. High-pressure synthesis and single-crystal structure elucidation of the indium oxide-borate In{sub 4}O{sub 2}B{sub 2}O{sub 7}

    Energy Technology Data Exchange (ETDEWEB)

    Ortner, Teresa S.; Vitzthum, Daniela; Heymann, Gunter; Huppertz, Hubert [Department of General, Inorganic and Theoretical Chemistry, Centre of Chemistry and Biomedicine (CCB), Leopold-Franzens-University Innsbruck (Austria)

    2017-12-29

    The indium oxide-borate In{sub 4}O{sub 2}B{sub 2}O{sub 7} was synthesized under high-pressure/high-temperature conditions at 12.5 GPa/1420 K using a Walker-type multianvil apparatus. Single-crystal X-ray structure elucidation showed edge-sharing OIn{sub 4} tetrahedra and B{sub 2}O{sub 7} units building up the oxide-borate. It crystallizes with Z = 8 in the monoclinic space group P2{sub 1}/n (no. 14) with a = 1016.54(3), b = 964.55(3), c = 1382.66(4) pm, and β = 109.7(1) . The compound was also characterized by powder X-ray diffraction and vibrational spectroscopy. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

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

    Directory of Open Access Journals (Sweden)

    Ian R Kelsall

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

  2. Gõtter, Grãber und Gelehrte

    Directory of Open Access Journals (Sweden)

    Pedro Moacyr Campos

    1953-09-01

    Full Text Available CERAM, (C. W.. — Gõtter, Grãber und Gelehrte, Rowohlt Verlag, Hamburg.,  1951, 494 págs. (Primeiro Parágrafo do Artigo Bem merecido foi o sucesso encontrado pelo livro de Ceram, Gotter, Graber und Gelehrte, ("Deuses, túmulos e eruditos", que alcançou a cifra de 106.000 exemplares entre novembro de 1949 e março de 1951, continuando a ser reimpresso após esta data.

  3. Tritium release behavior from neutron-irradiated Li{sub 2}TiO{sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Tanifuji, Takaaki; Yamaki, Daiju; Noda, Kenji [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Nasu, Shoichi

    1998-03-01

    Li{sub 2}TiO{sub 3} single-crystals with various size (1-2mm) were used as specimens. After the irradiation up to 4 x 10{sup 18} n/cm{sup 2} with thermal neutrons in JRR-2, tritium release from the Li{sub 2}TiO{sub 3} specimens in isothermal heating tests was continuously measured with a proportional counter. The tritium release in the range from 625K to 1373K seems to be controlled by bulk diffusion. The tritium diffusion coefficient (D{sub T}) in Li{sub 2}TiO{sub 3} was evaluated to be D{sub T}(cm{sup 2}/sec) = 0.100exp(-104(kJ/mol)/RT), 625Ksub 2}TiO{sub 3} is almost equal to those of Li{sub 2}O irradiated with thermal neutrons up to 2 x 10{sup 19} n/cm{sup 2}. It indicates that the tritium release performance of Li{sub 2}TiO{sub 3} is essentially good as Li{sub 2}O. (author)

  4. A single nucleotide mutation in Nppc is associated with a long bone abnormality in lbab mice.

    Science.gov (United States)

    Jiao, Yan; Yan, Jian; Jiao, Feng; Yang, Hongbin; Donahue, Leah Rae; Li, Xinmin; Roe, Bruce A; Stuart, John; Gu, Weikuan

    2007-04-17

    The long bone abnormality (lbab) mouse is a new autosomal recessive mutant characterized by overall smaller body size with proportionate dwarfing of all organs and shorter long bones. Previous linkage analysis has located the lbab mutation on chromosome 1 between the markers D1Mit9 and D1Mit488. A genome-based positional approach was used to identify a mutation associated with lbab disease. A total of 122 genes and expressed sequence tags at the lbab region were screened for possible mutation by using genomic DNA from lbabl/lbab, lbab/+, and +/+ B6 mice and high throughput temperature gradient capillary electrophoresis. A sequence difference was identified in one of the amplicons of gene Nppc between lbab/lbab and +/+ mice. One-step reverse transcriptase polymerase chain reaction was performed to validate the difference of Nppc in different types of mice at the mRNA level. The mutation of Nppc was unique in lbab/lbab mice among multiple mouse inbred strains. The mutation of Nppc is co-segregated with lbab disease in 200 progenies produced from heterozygous lbab/+ parents. A single nucleotide mutation of Nppc is associated with dwarfism in lbab/lbab mice. Current genome information and technology allow us to efficiently identify single nucleotide mutations from roughly mapped disease loci. The lbab mouse is a useful model for hereditary human achondroplasia.

  5. A single nucleotide mutation in Nppc is associated with a long bone abnormality in lbab mice

    Directory of Open Access Journals (Sweden)

    Roe Bruce A

    2007-04-01

    Full Text Available Abstract Background The long bone abnormality (lbab mouse is a new autosomal recessive mutant characterized by overall smaller body size with proportionate dwarfing of all organs and shorter long bones. Previous linkage analysis has located the lbab mutation on chromosome 1 between the markers D1Mit9 and D1Mit488. Results A genome-based positional approach was used to identify a mutation associated with lbab disease. A total of 122 genes and expressed sequence tags at the lbab region were screened for possible mutation by using genomic DNA from lbabl/lbab, lbab/+, and +/+ B6 mice and high throughput temperature gradient capillary electrophoresis. A sequence difference was identified in one of the amplicons of gene Nppc between lbab/lbab and +/+ mice. One-step reverse transcriptase polymerase chain reaction was performed to validate the difference of Nppc in different types of mice at the mRNA level. The mutation of Nppc was unique in lbab/lbab mice among multiple mouse inbred strains. The mutation of Nppc is co-segregated with lbab disease in 200 progenies produced from heterozygous lbab/+ parents. Conclusion A single nucleotide mutation of Nppc is associated with dwarfism in lbab/lbab mice. Current genome information and technology allow us to efficiently identify single nucleotide mutations from roughly mapped disease loci. The lbab mouse is a useful model for hereditary human achondroplasia.

  6. Synthesis of nanocrystalline Gd{sub 2}O{sub 2}NCN from a versatile single-source precursor

    Energy Technology Data Exchange (ETDEWEB)

    Ionescu, Emanuel; Wiehl, Leonore; Mera, Gabriela; Riedel, Ralf [Fachbereich Material- und Geowissenschaften, Technische Universitaet Darmstadt (Germany); Li, Wenjie [Fachbereich Material- und Geowissenschaften, Technische Universitaet Darmstadt (Germany); Center for Energy Harvesting Materials and Systems, Mechanical Engineering Department, Virginia Polytechnic Institute and State University, Blacksburg, VA (United States)

    2017-11-17

    Nanocrystalline Gd{sub 2}O{sub 2}NCN (P anti 3m1, crystallite size 30-40 nm) was synthesized upon ammonolysis of bis[[(N-carboxymethyl,N-carboxy-κO-methyl)amino-κN-ethyl]-glycinato( 3-)-κN,κO]gadolinium(III) (diethylenetriamine pentaacetic acid gadolinium(III) dihydrogen salt or gadopentetic acid, Gd-H{sub 2}DTPA hereafter) at 900 C. The conversion of Gd-H{sub 2}DTPA into Gd{sub 2}O{sub 2}NCN takes place in several steps, probably via transient formation of iminodiacetate-, glycinate-, and carbamate-containing complexes of Gd. Thermal treatment in air of Gd-H{sub 2}DTPA at 750 and 1300 C delivers nanocrystalline bixbyite-type Gd{sub 2}O{sub 3} (Ia anti 3, crystallite size 30-70 nm); in an argon or nitrogen atmosphere the formation of monoclinic Gd{sub 2}O{sub 3} (C2/m) was observed at 1300 C. The synthesized Gd{sub 2}O{sub 2}NCN converts upon thermal treatment in air, nitrogen, or argon atmosphere into monoclinic Gd{sub 2}O{sub 3} (C2/m). In ammonia atmosphere, Gd{sub 2}O{sub 2}NCN seems to be stable against decomposition, even upon prolonged exposure to 1000 C. This study indicates that Gd-H{sub 2}DTPA may be a robust, low-cost, and flexible precursor for nanoscaled Gd-based nanopowders. Moreover, precursor approaches based on metal complexes using H{sub 5}DTPA as a ligand are suggested as promising access pathways towards nanocrystalline materials in the M/O/C/N system. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Reversible migration of silver on memorized pathways in Ag-Ge{sub 40}S{sub 60} films

    Energy Technology Data Exchange (ETDEWEB)

    Orava, J., E-mail: jo316@cam.ac.uk, E-mail: alg13@cam.ac.uk; Greer, A. L., E-mail: jo316@cam.ac.uk, E-mail: alg13@cam.ac.uk [Department of Materials Science & Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS (United Kingdom); WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Kozicki, M. N. [School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, Arizona 85287-6206 (United States); Yannopoulos, S. N. [Foundation of Research and Technology Hellas - Institute of Chemical Engineering Sciences (FORTH/ICE-HT), Patras, P. O. Box 1414 (Greece)

    2015-07-15

    Reversible and reproducible formation and dissolution of silver conductive filaments are studied in Ag-photodoped thin-film Ge{sub 40}S{sub 60} subjected to electric fields. A tip-planar geometry is employed, where a conductive-atomic-force microscopy tip is the tip electrode and a silver patch is the planar electrode. We highlight an inherent “memory” effect in the amorphous chalcogenide solid-state electrolyte, in which particular silver-ion migration pathways are preserved “memorized” during writing and erasing cycles. The “memorized” pathways reflect structural changes in the photodoped chalcogenide film. Structural changes due to silver photodoping, and electrically-induced structural changes arising from silver migration, are elucidated using Raman spectroscopy. Conductive filament formation, dissolution, and electron (reduction) efficiency in a lateral device geometry are related to operation of the nano-ionic Programmable Metallization Cell memory and to newly emerging chalcogenide-based lateral geometry MEMS technologies. The methods in this work can also be used for qualitative multi-parameter sampling of metal/amorphous-chalcogenide combinations, characterizing the growth/dissolution rates, retention and endurance of fractal conductive filaments, with the aim of optimizing devices.

  8. Nanocrystalline Si pathway induced unipolar resistive switching behavior from annealed Si-rich SiN{sub x}/SiN{sub y} multilayers

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Xiaofan; Ma, Zhongyuan, E-mail: zyma@nju.edu.cn; Yang, Huafeng; Yu, Jie; Wang, Wen; Zhang, Wenping; Li, Wei; Xu, Jun; Xu, Ling; Chen, Kunji; Huang, Xinfan; Feng, Duan [National Laboratory of Solid State Microstructures, Jiangsu Provincial Key Laboratory of Photonic Electronic Materials Sciences and Technology, School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China)

    2014-09-28

    Adding a resistive switching functionality to a silicon microelectronic chip is a new challenge in materials research. Here, we demonstrate that unipolar and electrode-independent resistive switching effects can be realized in the annealed Si-rich SiN{sub x}/SiN{sub y} multilayers with high on/off ratio of 10{sup 9}. High resolution transmission electron microscopy reveals that for the high resistance state broken pathways composed of discrete nanocrystalline silicon (nc-Si) exist in the Si nitride multilayers. While for the low resistance state the discrete nc-Si regions is connected, forming continuous nc-Si pathways. Based on the analysis of the temperature dependent I-V characteristics and HRTEM photos, we found that the break-and-bridge evolution of nc-Si pathway is the origin of resistive switching memory behavior. Our findings provide insights into the mechanism of the resistive switching behavior in nc-Si films, opening a way for it to be utilized as a material in Si-based memories.

  9. Genetic variation in the base excision repair pathway, environmental risk factors, and colorectal adenoma risk.

    Directory of Open Access Journals (Sweden)

    Roman Corral

    Full Text Available Cigarette smoking, high alcohol intake, and low dietary folate levels are risk factors for colorectal adenomas. Oxidative damage caused by these three factors can be repaired through the base excision repair pathway (BER. We hypothesized that genetic variation in BER might modify colorectal adenoma risk. In a sigmoidoscopy-based study, we examined associations between 182 haplotype tagging SNPs in 14 BER genes, and colorectal adenoma risk, and examined their potential role as modifiers of the effect cigarette smoking, alcohol intake, and dietary folate levels. Among all individuals, no statistically significant associations between BER SNPs and adenoma risk persisted after correction for multiple comparisons. However, among Asian-Pacific Islanders we observed two SNPs in FEN1 and one in NTHL1, and among African-Americans one SNP in APEX1 that were associated with colorectal adenoma risk. Significant associations were also observed between SNPs in the NEIL2 gene and rectal adenoma risk. Three SNPS modified the effect of smoking (MUTYH interaction p = 0.002; OGG1 interaction p = 0.013; FEN1 interaction p = 0.013, one SNP in LIG3 modified the effect of alcohol consumption (interaction p = 0.024 and two SNPs in LIG3 modified the effect of dietary folate (interaction p = 0.001 and p = 0.08 on colorectal adenoma risk. These findings support a role for genetic variants in the BER pathway as potential modifiers of colorectal adenoma risk. Our findings strengthen the role of oxidative damage induced by key lifestyle and dietary risk factors in colorectal adenoma formation.

  10. VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism

    Directory of Open Access Journals (Sweden)

    HyoYoung Kim

    2014-12-01

    Full Text Available Copy number variation (CNV or single nucleotide phlyorphism (SNP is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i the enrichment of genome contents in CNV; ii the physical distribution of CNV or SNP on chromosomes; iii the distribution of log2 ratio of CNVs with criteria of interested; iv the number of CNV or SNP per binning unit; v the distribution of homozygosity of SNP genotype; and vi cytomap of genes within CNV or SNP region.

  11. RareVar: A Framework for Detecting Low-Frequency Single-Nucleotide Variants.

    Science.gov (United States)

    Hao, Yangyang; Xuei, Xiaoling; Li, Lang; Nakshatri, Harikrishna; Edenberg, Howard J; Liu, Yunlong

    2017-07-01

    Accurate identification of low-frequency somatic point mutations in tumor samples has important clinical utilities. Although high-throughput sequencing technology enables capturing such variants while sequencing primary tumor samples, our ability for accurate detection is compromised when the variant frequency is close to the sequencer error rate. Most current experimental and bioinformatic strategies target mutations with ≥5% allele frequency, which limits our ability to understand the cancer etiology and tumor evolution. We present an experimental and computational modeling framework, RareVar, to reliably identify low-frequency single-nucleotide variants from high-throughput sequencing data under standard experimental protocols. RareVar protocol includes a benchmark design by pooling DNAs from already sequenced individuals at various concentrations to target variants at desired frequencies, 0.5%-3% in our case. By applying a generalized, linear model-based, position-specific error model, followed by machine-learning-based variant calibration, our approach outperforms existing methods. Our method can be applied on most capture and sequencing platforms without modifying the experimental protocol.

  12. Hydrostatic pressure (8 GPa) dependence of electrical resistivity of BaCo{sub 2}As{sub 2} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Ganguli, Chandreyee; Matsubayashi, Kazuyuki; Ohgushi, Kenya [Institute for Solid State Physics, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); Uwatoko, Yoshiya, E-mail: uwatoko@issp.u-tokyo.ac.jp [Institute for Solid State Physics, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); Kanagaraj, Moorthi [Centre for High Pressure Research, School of Physics, Bharathidasan University, Tiruchirappalli 620024 (India); Arumugam, Sonachalam, E-mail: sarumugam1963@yahoo.com [Centre for High Pressure Research, School of Physics, Bharathidasan University, Tiruchirappalli 620024 (India)

    2013-10-15

    Graphical abstract: - Highlights: • Single crystals of BaCo{sub 2}As{sub 2} were grown by CoAs self-flux method. • We have studied pressure effects (8 GPa) on dc electrical resistivity of BaCo{sub 2}As{sub 2}. • On applied external pressure BaCo{sub 2}As{sub 2} remains a metallic state up to 8 GPa. • Superconductivity is absent in BaCo{sub 2}As{sub 2} because of its proximity to ferromagnetism. - Abstract: The pressure dependence of the electrical resistivity of BaCo{sub 2}As{sub 2} single crystal as a function of temperature was measured at ambient and high pressures up to 8 GPa for the first time using cubic anvil high pressure cell. It is observed that at room temperature the resistivity monotonically decreases with increasing pressure and it remains in the metallic state even at an applied pressure of 8 GPa. From the temperature dependence of the resistivity measurements under pressure, we found that superconductivity is absent up to 8 GPa. The value of the electron's scattering factor (A) is found to be large at ambient pressure and it decreases with the application of pressure, indicating that the substantial electron correlation effect of BaCo{sub 2}As{sub 2} is reduced under pressure, revealing a dramatic change of density of states at the Fermi energy.

  13. A Comprehensive Experiment for Molecular Biology: Determination of Single Nucleotide Polymorphism in Human REV3 Gene Using PCR-RFLP

    Science.gov (United States)

    Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

    2017-01-01

    Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of…

  14. Photocatalytic applications of Cr{sub 2}S{sub 3} synthesized from single and multi-source precursors

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, Wajid [Department of Chemistry, Quaid-i-Azam University, 45320, Islamabad (Pakistan); Badshah, Amin, E-mail: aminbadshah@qau.edu.pk [Department of Chemistry, Quaid-i-Azam University, 45320, Islamabad (Pakistan); Hussain, Raja Azadar; Imtiaz-ud-Din [Department of Chemistry, Quaid-i-Azam University, 45320, Islamabad (Pakistan); Aleem, Muhammad Adeel [The Pakistan Institute of Engineering and Applied Sciences (PIEAS) (Pakistan); Bahadur, Ali [Department of Chemistry, Quaid-i-Azam University, 45320, Islamabad (Pakistan); Iqbal, Shahid [School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049 (China); Farooq, Muhammad Umar; Ali, Hassan [Department of Chemistry, Quaid-i-Azam University, 45320, Islamabad (Pakistan)

    2017-06-15

    Most of the material research work is pertinent to the synthesis of transition-metal sulfides nanoparticles but here the studies are limited to the synthesis of chromium sulfide. However, the preparation method, presented in this work, may be extended to other metal chalcogenides nanoparticles for various potential applications. The ligand (precursor), 1-(2-chloro-4-nitrophenyl)-3,3-chlorobenzoyl and Cr{sub 2}S{sub 3} have been synthesized initially from single source precursor and then from multi source precursors. The target was to alter the morphologies of nanomaterial while altering the synthetic route and that was successfully achieved. Chromium sulfide nano-rods were synthesized using single source precursors while nanoparticles were fabricated using multi source precursors. Characterization were carried out through {sup 1}H and {sup 13}C NMR, scanning electron microscopy (SEM), transmission electron microscopy (TEM), powder X-ray diffraction microscopy (PXRD), energy dispersive X-ray spectroscopy (EDX), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and high resolution transmission electron microscopy (HRTEM). Our objective is to change the morphologies by changing the synthetic route so that is why further applications were done only for multi-source product, denying single source product. The metal sulfides nanoparticles exhibit higher activity than their bulk material for the photocatalytic degradation of organic dyes under visible-light irradiation. So, photocatalytic activity was successfully achieved under direct sunlight against five different cationic and anionic organic dyes including malachite green (MG), methylene blue (MB), rhodamine B (RhB), methyl violet (MV) and methyl orange (MO). These organic dyes MV, MG, MB, and RB were almost diminished or decolorized by Cr{sub 2}S{sub 3} within 110, 90, 100, and 130, minutes, respectively expect MO. - Highlights: • Synthesis of Cr{sub 2}S{sub 3} from single and multisource precursors is

  15. Nucleotide sequence preservation of human mitochondrial DNA

    International Nuclear Information System (INIS)

    Monnat, R.J. Jr.; Loeb, L.A.

    1985-01-01

    Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mp11; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five normal donors. Both between- and within-individual differences were identified. Between-individual differences were identified in approximately = to 1/200 nucleotides. In contrast, only one within-individual difference was identified in 49 kilobases of nucleotide sequence information. This high degree of mitochondrial nucleotide sequence homogeneity in human somatic cells is in marked contrast to the rapid evolutionary divergence of human mitochondrial DNA and suggests the existence of mechanisms for the concerted preservation of mammalian mitochondrial DNA sequences in single organisms

  16. Single-crystal X-ray diffraction study of Cs{sub 2}Er[Si{sub 6}O{sub 14}]F and Cs{sub 2}Er[Si{sub 4}O{sub 10}]F

    Energy Technology Data Exchange (ETDEWEB)

    Dabic, Predrag; Kremenovic, Aleksandar; Vulic, Predag [Belgrade Univ. (Serbia). Lab. of Crystallography; Kahlenberg, Volker; Schmidmair, Daniela [Innsbruck Univ. (Austria). Inst. of Mineralogy and Petrography

    2016-07-01

    Single-crystal growth experiments in the system CsF-Er{sub 2}O{sub 3}-SiO{sub 2} resulted in the simultaneous crystallization of two chemically related compounds within the same run: Cs{sub 2}Er[Si{sub 6}O{sub 14}]F (phase I) and Cs{sub 2}Er[Si{sub 4}O{sub 10}]F (phase II). They represent the first examples for cesium erbium silicates containing fluorine. Basic crystallographic data are - phase I: space group Cmca, a=17.2556(6) Aa, b=24.6565(7) Aa, c=14.4735(5) Aa, V=6157.9(3) Aa{sup 3}, Z=16; phase II: space group Pnma, a=22.3748(7) Aa, b=8.8390(2) Aa, c=11.9710(4) Aa, V=2367.5(1) Aa{sup 3}, Z=8. The structures were determined by direct methods and refined to residuals of R(vertical stroke F vertical stroke)=0.0229 for 2920 (phase I) and 0.0231 for 2314 (phase II) independent observed reflections with I>2σ(I). The structure of phase I represents a previously unknown structure type with a three dimensional tetrahedral framework consisting of Q{sup 3} and Q{sup 4} groups in the ratio 2:1. Basic building units of the network are unbranched sechser single-chains running parallel to [001]. The network can be conveniently built up from the condensation of tetrahedral layers parallel to (010) or (100), respectively. The crystal structure of phase II can be classified as a tubular or columnar chain silicate indicating that the backbones of the structure are multiple chains of silicate tetrahedra. This structure is isotypic to a Cs{sub 2}Y[Si{sub 4}O{sub 10}]F, a compound that has been characterized previously. Alternatively, both compounds can be described as mixed octahedral-tetrahedral frameworks, which can be classified according to their polyhedral microensembles. A topological analysis of both nets is presented.

  17. Frequency of single nucleotide polymorphisms of some immune response genes in a population sample from São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Léa Campos de Oliveira

    2011-09-01

    Full Text Available Objective: To present the frequency of single nucleotide polymorphismsof a few immune response genes in a population sample from SãoPaulo City (SP, Brazil. Methods: Data on allele frequencies ofknown polymorphisms of innate and acquired immunity genes werepresented, the majority with proven impact on gene function. Datawere gathered from a sample of healthy individuals, non-HLA identicalsiblings of bone marrow transplant recipients from the Hospital dasClínicas da Faculdade de Medicina da Universidade de São Paulo,obtained between 1998 and 2005. The number of samples variedfor each single nucleotide polymorphism analyzed by polymerasechain reaction followed by restriction enzyme cleavage. Results:Allele and genotype distribution of 41 different gene polymorphisms,mostly cytokines, but also including other immune response genes,were presented. Conclusion: We believe that the data presentedhere can be of great value for case-control studies, to define whichpolymorphisms are present in biologically relevant frequencies and toassess targets for therapeutic intervention in polygenic diseases witha component of immune and inflammatory responses.

  18. Condensing the information in DNA with double-headed nucleotides

    DEFF Research Database (Denmark)

    Hornum, Mick; Sharma, Pawan K; Reslow-Jacobsen, Charlotte

    2017-01-01

    A normal duplex holds as many Watson-Crick base pairs as the number of nucleotides in its constituent strands. Here we establish that single nucleotides can be designed to functionally imitate dinucleotides without compromising binding affinity. This effectively allows sequence information...

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

    Directory of Open Access Journals (Sweden)

    Apurva Barve

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

  20. Genetic Variants in the Wnt/β-Catenin Signaling Pathway as Indicators of Bladder Cancer Risk.

    Science.gov (United States)

    Pierzynski, Jeanne A; Hildebrandt, Michelle A; Kamat, Ashish M; Lin, Jie; Ye, Yuanqing; Dinney, Colin P N; Wu, Xifeng

    2015-12-01

    Genetic factors that influence bladder cancer risk remain largely unknown. Previous research has suggested that there is a strong genetic component underlying the risk of bladder cancer. The Wnt/β-catenin signaling pathway is a key modulator of cellular proliferation through its regulation of stem cell homeostasis. Furthermore, variants in the Wnt/β-catenin signaling pathway have been implicated in the development of other cancers, leading us to believe that this pathway may have a vital role in bladder cancer development. A total of 230 single nucleotide polymorphisms in 40 genes in the Wnt/β-catenin signaling pathway were genotyped in 803 bladder cancer cases and 803 healthy controls. A total of 20 single nucleotide polymorphisms were nominally significant for risk. Individuals with 2 variants of LRP6: rs10743980 were associated with a decreased risk of bladder cancer in the recessive model in the initial analysis (OR 0.76, 95% CI 0.58-0.99, p=0.039). This was validated using the bladder genome-wide association study chip (OR 0.51, 95% CI 0.27-1.00, p=0.049 and for combined analysis p=0.007). Together these findings implicate variants in the Wnt/β-catenin stem cell pathway as having a role in bladder cancer etiology. Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  1. Effect of BCHE single nucleotide polymorphisms on lipid metabolism markers in women

    Directory of Open Access Journals (Sweden)

    Jéssica de Oliveira

    2017-05-01

    Full Text Available Abstract Butyrylcholinesterase (BChE activity and polymorphisms in its encoding gene had previously been associated with metabolic traits of obesity. This study investigated the association of three single nucleotide polymorphisms (SNPs in the BCHE gene: -116G > A (rs1126680, 1615GA (rs1803274, 1914A 0.05. The dominant and recessive models were tested, and different effects were found. The -116A allele showed a dominant effect in BChE activity reduction in both non-obese and obese women (p = 0.045 and p G and 1615GA SNPs influenced the TG levels only in obese women. The 1914G and the 1615A alleles were associated with decreased plasma levels of TG. Thus, our results suggest that the obesity condition, characterized by loss of energy homeostasis, is modulated by BCHE polymorphisms.

  2. Single-phase ceramics with La{sub 1-x}Sr{sub x}Ga{sub 1-y}Mg{sub y}O{sub 3-{delta}} composition from precursors obtained by mechanosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Moure, A.; Tartaj, J.; Moure, C. [Instituto de Ceramica y Vidrio, CSIC, C/Kelsen 5, 28049 Madrid (Spain); Castro, A. [Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Ines de la Cruz, 3 Cantoblanco, 28049 Madrid (Spain)

    2009-03-15

    Dense ceramics with La{sub 0.80}Sr{sub 0.20}Ga{sub 0.85}Mg{sub 0.15}O{sub 2.825} and La{sub 0.80}Sr{sub 0.15}Ga{sub 0.85}Mg{sub 0.20}O{sub 2.825} compositions have been prepared by sintering of mechanosynthesized precursors. The perovskite is synthesized after 85 h of milling in a planetary mill. Single phases have been obtained at conditions that are not possible if traditional solid-state reaction (SSR) method is used. The influence of milling time and composition in the reactivity of the precursors is studied. Highest purity is obtained in Sr = 0.15 and Mg = 0.20 composition, with relative density higher than 97%. The total elimination of typical secondary phases for these compositions, as SrLaGaO{sub 4} and SrLaGa{sub 3}O{sub 7}, allows the total conductivity of the ceramics to be improved. The influence of the grain size and the nature of the grain boundaries on the electrical characteristic of the ceramics are also discussed. (author)

  3. Growth and characterization of the La{sub 3}Ga{sub 4.85}Fe{sub 0.15}SiO{sub 14} piezoelectric single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Dou, Renqin [Chinese Academy of Sciences, The Key Laboratory of Photonic Devices and Materials, Anhui Institute of Optics and Fine Mechanics, Hefei, Anhui Province (China); University of Science and Technology of China, Hefei (China); Liu, Wenpeng; Zhang, Qingli; Ding, Shoujun; Sun, Dunlu [Chinese Academy of Sciences, The Key Laboratory of Photonic Devices and Materials, Anhui Institute of Optics and Fine Mechanics, Hefei, Anhui Province (China); Zhang, Qi [Anhui Firesky Crystal Science and Technology Co. Ltd, Tongling (China); Shi, Zibin [26th Institute of China Electronics Technology Group Corporation, Chongqing (China); Wang, Jiyang [Shandong University, State Key Laboratory of Crystal Materials, Jinan (China)

    2017-01-15

    A new piezoelectric single crystal La{sub 3}Ga{sub 4.85}Fe{sub 0.15}SiO{sub 14} (LGFS) was grown by the Czochralski method firstly. Its structural parameters were obtained by Rietveld refinement to the X-ray diffraction. The effective segregation coefficient k{sub eff} of Fe in the LGFS was determined to be 0.6. The cost of LGFS is reduced due to the doping of cheap Fe. The crystal density was measured to be 5.7 g cm{sup -3} by the buoyancy method. The defect structure of LGFS crystal was investigated by the chemical etching with 85% H{sub 2}SO{sub 4} etchant. Dislocation etching pit patterns of LGFS crystal are consistent with the corresponding atomic arrangement schematics. Compared with LGS, LGN, LGT, and LGAS crystal, the LGFS crystal exhibits outstanding dielectric and piezoelectric properties, and ε {sub 11}, ε {sub 33}, d{sub 11}, and d{sub 14} are 20.86, 51.99, 6.5 pC/N, and -5.10 pC/N, respectively. Therefore, LGFS may be a new potential piezoelectric crystal with high performance and low expense. (orig.)

  4. Ku80-deleted cells are defective at base excision repair

    Energy Technology Data Exchange (ETDEWEB)

    Li, Han [The University of Texas Health Science Center at San Antonio, The Institute of Biotechnology, The Department of Molecular Medicine, 15355 Lambda Drive, San Antonio, TX 78245-3207 (United States); Tumor Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029 (Spain); Marple, Teresa [The University of Texas Health Science Center at San Antonio, The Institute of Biotechnology, The Department of Molecular Medicine, 15355 Lambda Drive, San Antonio, TX 78245-3207 (United States); Hasty, Paul, E-mail: hastye@uthscsa.edu [The University of Texas Health Science Center at San Antonio, The Institute of Biotechnology, The Department of Molecular Medicine, 15355 Lambda Drive, San Antonio, TX 78245-3207 (United States); Tumor Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029 (Spain)

    2013-05-15

    Graphical abstract: - Highlights: • Ku80-deleted cells are hypersensitive to ROS and alkylating agents. • Cells deleted for Ku80, but not Ku70 or Lig4, have reduced BER capacity. • OGG1 rescues hypersensitivity to H{sub 2}O{sub 2} and paraquat in Ku80-mutant cells. • Cells deleted for Ku80, but not Lig4, are defective at repairing AP sites. • Cells deleted for Ku80, but not Lig4 or Brca2 exon 27, exhibit increased PAR. - Abstract: Ku80 forms a heterodimer with Ku70, called Ku, that repairs DNA double-strand breaks (DSBs) via the nonhomologous end joining (NHEJ) pathway. As a consequence of deleting NHEJ, Ku80-mutant cells are hypersensitive to agents that cause DNA DSBs like ionizing radiation. Here we show that Ku80 deletion also decreased resistance to ROS and alkylating agents that typically cause base lesions and single-strand breaks (SSBs). This is unusual since base excision repair (BER), not NHEJ, typically repairs these types of lesions. However, we show that deletion of another NHEJ protein, DNA ligase IV (Lig4), did not cause hypersensitivity to these agents. In addition, the ROS and alkylating agents did not induce γ-H2AX foci that are diagnostic of DSBs. Furthermore, deletion of Ku80, but not Lig4 or Ku70, reduced BER capacity. Ku80 deletion also impaired BER at the initial lesion recognition/strand scission step; thus, involvement of a DSB is unlikely. Therefore, our data suggests that Ku80 deletion impairs BER via a mechanism that does not repair DSBs.

  5. Comparative study of optical and scintillation properties of YVO{sub 4}, (Lu{sub 0.5}Y{sub 0.5})VO{sub 4}, and LuVO{sub 4} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Fujimoto, Yutaka, E-mail: fuji-you@tagen.tohoku.ac.j [IMRAM, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Yanagida, Takayuki; Yokota, Yuui; Chani, Valery [IMRAM, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Kochurikhin, Vladimir V. [General Physics Institute, 38 Vavilov Street, 119991, Federation, Moscow (Russian Federation); Yoshikawa, Akira [IMRAM, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); NICHe, Tohoku University, 6-6-10 Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan)

    2011-04-11

    Optical and scintillation properties of YVO{sub 4}, (Lu{sub 0.5}Y{sub 0.5})VO{sub 4}, and LuVO{sub 4} single crystals grown by the Czochralski (CZ) method with RF heating system are compared. All vanadate crystals show high transmittance ({approx}80%) in the 400-900 nm wavelength range. In both photo- and radio-luminescence spectra, intense peak around 400-500 nm, which was ascribed to the transition from triplet state of VO{sub 4}{sup 3-}, was clearly observed. The main decay time component was about 38 {mu}s (YVO{sub 4}), 18 {mu}s ((Lu{sub 0.5}Y{sub 0.5})VO{sub 4}), and 17 {mu}s (LuVO{sub 4}) under 340 nm excitation. The scintillation light yields of YVO{sub 4}, (Lu{sub 0.5}Y{sub 0.5})VO{sub 4}, and LuVO{sub 4} crystals (obtained from the {sup 137}Cs excited pulse height spectra) were evaluated to be about 11,200, 10,700, and 10,300 ph/MeV, respectively.

  6. Single Nucleotide Polymorphisms in Common Bean: Their Discovery and Genotyping Using a Multiplex Detection System

    Directory of Open Access Journals (Sweden)

    E. Gaitán-Solís

    2008-11-01

    Full Text Available Single nucleotide polymorphism (SNP markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean ( L. by comparing sequences from coding and noncoding regions obtained from the GenBank and genomic DNA and to compare sequencing results with those obtained using single base extension (SBE assays on the Luminex-100 system for use in high-throughput germplasm evaluation. We assessed the frequency of SNPs in 47 fragments of common bean DNA, using SBE as the evaluation methodology. We conducted a sequence analysis of 10 genotypes of cultivated and wild beans belonging to the Mesoamerican and Andean genetic pools of . For the 10 genotypes evaluated, a total of 20,964 bp of sequence were analyzed in each genotype and compared, resulting in the discovery of 239 SNPs and 133 InDels, giving an average SNP frequency of one per 88 bp and an InDel frequency of one per 157 bp. This is the equivalent of a nucleotide diversity (θ of 6.27 × 10. Comparisons with the SNP genotypes previously obtained by direct sequencing showed that the SBE assays on the Luminex-100 were accurate, with 2.5% being miscalled and 1% showing no signal. These results indicate that the Luminex-100 provides a high-throughput system that can be used to analyze SNPs in large samples of genotypes both for purposes of assessing diversity and also for mapping studies.

  7. The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions.

    Science.gov (United States)

    Yates, Christopher M; Sternberg, Michael J E

    2013-11-01

    Non-synonymous single nucleotide polymorphisms (nsSNPs) are single base changes leading to a change to the amino acid sequence of the encoded protein. Many of these variants are associated with disease, so nsSNPs have been well studied, with studies looking at the effects of nsSNPs on individual proteins, for example, on stability and enzyme active sites. In recent years, the impact of nsSNPs upon protein-protein interactions has also been investigated, giving a greater insight into the mechanisms by which nsSNPs can lead to disease. In this review, we summarize these studies, looking at the various mechanisms by which nsSNPs can affect protein-protein interactions. We focus on structural changes that can impair interaction, changes to disorder, gain of interaction, and post-translational modifications before looking at some examples of nsSNPs at human-pathogen protein-protein interfaces and the analysis of nsSNPs from a network perspective. © 2013.

  8. Fergusonite-type CeNbO{sub 4+δ}: Single crystal growth, symmetry revision and conductivity

    Energy Technology Data Exchange (ETDEWEB)

    Bayliss, Ryan D. [Department of Materials, Imperial College London, Prince Consort Road, London, SW7 2BP (United Kingdom); Pramana, Stevin S.; An, Tao; Wei, Fengxia; Kloc, Christian L. [School of Materials Science and Engineering, 50 Nanyang Avenue, Nanyang Technological University, 639798 (Singapore); White, Andrew J.P. [Chemical Crystallography Laboratory, Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ (United Kingdom); Skinner, Stephen J. [Department of Materials, Imperial College London, Prince Consort Road, London, SW7 2BP (United Kingdom); White, Timothy J. [School of Materials Science and Engineering, 50 Nanyang Avenue, Nanyang Technological University, 639798 (Singapore); Baikie, Tom, E-mail: tbaikie@ntu.edu.sg [School of Materials Science and Engineering, 50 Nanyang Avenue, Nanyang Technological University, 639798 (Singapore)

    2013-08-15

    Large fergusonite-type (ABO{sub 4}, A=Ce, B=Nb) oxide crystals, a prototype electrolyte composition for solid oxide fuel cells (SOFC), were prepared for the first time in a floating zone mirror furnace under air or argon atmospheres. While CeNbO{sub 4} grown in air contained CeNbO{sub 4.08} as a minor impurity that compromised structural analysis, the argon atmosphere yielded a single phase crystal of monoclinic CeNbO{sub 4}, as confirmed by selected area electron diffraction, powder and single crystal X-ray diffraction. The structure was determined in the standard space group setting C12/c1 (No. 15), rather than the commonly adopted I12/a1. AC impedance spectroscopy conducted under argon found that stoichiometric CeNbO{sub 4} single crystals showed lower conductivity compared to CeNbO{sub 4+δ} confirming interstitial oxygen can penetrate through fergusonite and is responsible for the higher conductivity associated with these oxides. - Graphical abstract: Large fergusonite-type CeNbO{sub 4} crystals were prepared for the first time in a floating zone mirror furnace. Crystal growth in an argon atmosphere yielded a single phase monoclinic CeNbO4, as confirmed by selected area electron diffraction, powder and single crystal X-ray diffraction. The structure was determined in the standard space group setting C12/c1 (No. 15), rather than the commonly adopted I12/a1. AC impedance spectroscopy found CeNbO{sub 4} single crystals showed lower conductivity compared to CeNbO{sub 4+δ} confirming interstitial oxygen can penetrate through fergusonite and is responsible for the higher conductivity associated with these oxides. Highlights: • Preparation of single crystals of CeNbO{sub 4} using a floating zone mirror furnace. • Correction to the crystal symmetry of the monoclinic form of CeNbO{sub 4}. • Report the conductivity of a single crystal of CeNbO{sub 4}.

  9. A Locked Nucleic Acid Probe Based on Selective Salt-Induced Effect Detects Single Nucleotide Polymorphisms

    Directory of Open Access Journals (Sweden)

    Jing Zhang

    2015-01-01

    Full Text Available Detection of single based genetic mutation by using oligonucleotide probes is one of the common methods of detecting single nucleotide polymorphisms at known loci. In this paper, we demonstrated a hybridization system which included a buffer solution that produced selective salt-induced effect and a locked nucleic acid modified 12 nt oligonucleotide probe. The hybridization system is suitable for hybridization under room temperature. By using magnetic nanoparticles as carriers for PCR products, the SNPs (MDR1 C3435T/A from 45 volunteers were analyzed, and the results were consistent with the results from pyrophosphoric acid sequencing. The method presented in this paper differs from the traditional method of using molecular beacons to detect SNPs in that it is suitable for research institutions lacking real-time quantitative PCR detecting systems, to detect PCR products at room temperature.

  10. Timing characteristics of Ce doped Gd{sub 3}Ga{sub 3}Al{sub 2}O{sub 12} single crystals in comparison with CsI(Tl) scintillators

    Energy Technology Data Exchange (ETDEWEB)

    Tyagi, M.; Singh, A.K.; Singh, S.G.; Sen, S.; Gadkari, S.C. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085 (India); Desai, V.V.; Nayak, B.K. [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085 (India)

    2015-10-15

    Single crystals of Gd{sub 3}Ga{sub 3}Al{sub 2}O{sub 12}:Ce with B codopants were successfully grown using the Czochralski technique. The timing characteristics of the crystal was measured by coupling the crystal to photomultiplier tubes (PMT) or silicon photodiodes [Si(PIN)]. The two prompt γ-rays emitted in a cascade from {sup 60}Co or {sup 22}Na source were detected in coincidence using Gd{sub 3}Ga{sub 3}Al{sub 2}O{sub 12}:Ce,B crystal detectors and a BaF{sub 2} detector. The time resolution of these crystals are observed to be better than that measured for CsI:Tl crystal coupled to PMT or Si(PIN) in an identical measurement setup. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  11. Analyzing a single nucleotide polymorphism in schizophrenia: a meta-analysis approach

    Directory of Open Access Journals (Sweden)

    Falola O

    2017-08-01

    Full Text Available Oluwadamilare Falola,1 Victor Chukwudi Osamor,1,2 Marion Adebiyi,1,2 Ezekiel Adebiyi1,2 1Covenant University Bioinformatics Research (CUBRe, 2Department of Computer and Information Sciences, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria Background: Schizophrenia is a severe mental disorder affecting >21 million people worldwide. Some genetic studies reported that single nucleotide polymorphism (SNP involving variant rs1344706 from the ZNF804A gene in human beings is associated with the risk of schizophrenia in several populations. Similar results tend to conflict with other reports in literature, indicating that no true significant association exists between rs1344706 and schizophrenia. We seek to determine the level of association of this SNP with schizophrenia in the Asian population using more recent genome-wide association study (GWAS datasets. Methods: Applying a computational approach with inclusion of more recent GWAS datasets, we conducted a meta-analysis to examine the level of association of SNP rs1344706 and the risk of schizophrenia disorder among the Asian population constituting Chinese, Indonesians, Japanese, Kazakhs and Singaporeans. For a total of 21 genetic studies, including a total of 28,842 cases and 35,630 controls, regression analysis, publication bias, Cochran’s Q and I2 tests were performed. The DerSimonian and Laird random-effects model was used to assess the association of the genetic variant to schizophrenia. Leave-one-out sensitivity analysis was also conducted to determine the influence of each study on the final outcome of the association study. Results: Our summarized analysis for Asian population revealed a pooled odds ratio of 1.06, 95% confidence interval of 1.01–1.11 and two-tailed P-value of 0.0228. Our test for heterogeneity showed the presence of large heterogeneity (I2=53.44%, P =0.00207 and Egger’s regression test (P =0.8763 and Begg’s test (P =0

  12. Lebensdauer von Stahlseilen beim kombinierten Lauf über Treib- und Ablenkscheiben unterschiedlicher Rillenform

    OpenAIRE

    Berner, Oliver Roger

    2011-01-01

    Die Lebensdauer von Stahldrahtseilen in Treibscheibenaufzügen wird von unterschiedlichen Faktoren beeinflusst. Bei allen Anwendungen, bei denen Seile über Rollen laufen, erfahren die Seile eine Zug- und Biegebeanspruchung, die zu einer Materialermüdung und zu einem Verschleiß der Drähte an der Seiloberfläche und im Inneren der Seile führt. Darüber hinaus findet man bei Treibscheibenaufzügen systembedingt weitere anwendungsspezifische Beanspruchungen, die zu einer zusätzlichen Lebensdauerminde...

  13. Bioinformatic Analysis of Deleterious Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs in the Coding Regions of Human Prion Protein Gene (PRNP

    Directory of Open Access Journals (Sweden)

    Kourosh Bamdad

    2016-12-01

    Full Text Available Background & Objective: Single nucleotide polymorphisms are the cause of genetic variation to living organisms. Single nucleotide polymorphisms alter residues in the protein sequence. In this investigation, the relationship between prion protein gene polymorphisms and its relevance to pathogenicity was studied. Material & Method: Amino acid sequence of the main isoform from the human prion protein gene (PRNP was extracted from UniProt database and evaluated by FoldAmyloid and AmylPred servers. All non-synonymous single nucleotide polymorphisms (nsSNPs from SNP database (dbSNP were further analyzed by bioinformatics servers including SIFT, PolyPhen-2, I-Mutant-3.0, PANTHER, SNPs & GO, PHD-SNP, Meta-SNP, and MutPred to determine the most damaging nsSNPs. Results: The results of the first structure analyses by FoldAmyloid and AmylPerd servers implied that regions including 5-15, 174-178, 180-184, 211-217, and 240-252 were the most sensitive parts of the protein sequence to amyloidosis. Screening all nsSNPs of the main protein isoform using bioinformatic servers revealed that substitution of Aspartic acid with Valine at position 178 (ID code: rs11538766 was the most deleterious nsSNP in the protein structure. Conclusion:  Substitution of the Aspartic acid with Valine at position 178 (D178V was the most pathogenic mutation in the human prion protein gene. Analyses from the MutPred server also showed that beta-sheets’ increment in the secondary structure was the main reason behind the molecular mechanism of the prion protein aggregation.

  14. Impact of Mutual Coupling and Polarization of Antennas on BER Performances of Spatial Multiplexing MIMO Systems

    Directory of Open Access Journals (Sweden)

    Jianfeng Zheng

    2012-01-01

    Full Text Available This paper is aimed at studying the impacts of mutual coupling, matching networks, and polarization of antennas on performances of Multiple-Input Multiple-Output (MIMO systems employing Spatial Multiplexing (SM. In particular, the uncoded average Bit Error Rate (BER of MIMO systems is investigated. An accurate signal analysis framework based on circuit network parameters is presented to describe the transmit/receive characteristics of the matched/unmatched antenna array. The studied arrays consist of matched/unmatched compact copolarization and polarization diversity antenna array. Monte-Carlo numerical simulations are used to study the BER performances of the SM MIMO systems using maximum-likelihood and/or zero-forcing detection schemes. The simulation results demonstrate that the use of matching networks can improve the BER performance of SM MIMO systems significantly, and the BER performance deterioration due to antenna orientation randomness can be compensated by use of polarization diversity antenna arrays.

  15. Supplementary Material for: The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara; Meier, Stuart; Gehring, Christoph A

    2016-01-01

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

  16. Rise and fall of ferromagnetism in O-irradiated Al{sub 2}O{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Li, Qiang [State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026 (China); China Spallation Neutron Source, Institute of High Energy Physics, Chinese Academy of Sciences, Dongguan 523803 (China); Xu, Juping; Liu, Jiandang; Du, Huaijiang; Ye, Bangjiao, E-mail: bjye@ustc.edu.cn [State Key Laboratory of Particle Detection and Electronics, University of Science and Technology of China, Hefei 230026 (China)

    2015-06-21

    In dilute magnetic semiconductors studies, sapphire was usually used as non-magnetic substrate for films. We observed weak ferromagnetic component in Al{sub 2}O{sub 3} single crystal substrate, and excluded the possibility of ferromagnetic contaminations carefully by inductively coupled plasma mass spectrometry and X-ray photoelectron spectroscopy. The ferromagnetism rise and fall during the process of annealing-oxygen irradiation-annealing of the sapphire. The ferromagnetic changes are consistent with Al-vacancy related defects detected by positron annihilation spectroscopy. With first-principle calculations, we confirm that Al-vacancy can introduce magnetic moment for 3 μB in Al{sub 2}O{sub 3} crystal and form stable V{sub Al}-V{sub Al} ferromagnetic coupling at room temperature.

  17. Effects of artificial holes in very large single-grain Y{sub 1.5}Ba{sub 2}Cu{sub 3}O{sub 7-y} bulk superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Park, S. D.; Jun, B. H.; Kim, C. J. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Park, H. W. [Korea University of Technology and Education, Cheonan (Korea, Republic of)

    2017-09-15

    The effects of artificial holes on the trapped magnetic fields and magnetic levitation forces of very large single-grain Y{sub 1.5}Ba{sub 2}Cu{sub 3}O{sub 7-y} (Y1.5) bulk superconductors were studied. Artificial holes were made for Y1.5 powder compacts by die pressing using cylindrical dies with a diameter of 30 mm or 40 m, or rectangular dies with a side length of 50 mm. The single grain Y1.5 bulk superconductors (25 mm, 33 mm in diameter and 42 mm in side length) with artificial holes were fabricated using a top-seeded melt growth (TSMG) process for the die-pressed Y1.5 powder compacts. The magnetic levitation forces at 77 K of the 25 mm single grain Y1.5 samples with one (diameters of 4.2 mm) or six artificial holes (diameters of 2.5 mm) were 10-17% higher than that of the Y1.5 sample without artificial holes. The trapped magnetic fields at 77 K of the Y1.5 samples with artificial holes were also 9.6-18% higher than that of the Y1.5 sample without artificial holes. The 33 mm and 42 mm single grain Y1.5 samples with artificial holes (2.5 mm and 4.2 mm in diameter) also showed trapped magnetic fields 10-13% higher than that of the Y1.5 samples without artificial holes in spite of the reduced superconducting volume fraction due to the presence of artificial holes. The property enhancement in the large single grain Y1.5 bulk superconductors appears to be attributed to the formation of the pore-free regions near the artificial holes and the homogeneous oxygen distribution in the large Y123 grains.

  18. Determination of intrinsic polarization for K{sub 2}ZnCl{sub 4} single crystal grown by Czochralski technique for ferroelectric applications

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Sonu [Crystal Lab, Department of Physics & Astrophysics, University of Delhi, Delhi-7 (India); Ray, Geeta [Crystal Lab, Department of Physics & Astrophysics, University of Delhi, Delhi-7 (India); Physics Department, Miranda House, University of Delhi, Delhi-7 (India); Sinha, Nidhi [Crystal Lab, Department of Physics & Astrophysics, University of Delhi, Delhi-7 (India); Department of Electronics, SGTB Khalsa College, University of Delhi, Delhi-7 (India); Kumar, Binay, E-mail: b3kumar69@yahoo.co.in [Crystal Lab, Department of Physics & Astrophysics, University of Delhi, Delhi-7 (India)

    2017-04-01

    Large sized single crystal of K{sub 2}ZnCl{sub 4} (KZC) was grown by Czochralski (Cz) technique. Structural parameters of KZC were determined by Single crystal X-ray diffraction (SCXRD). From DSC analysis and temperature dependent dielectric measurement, KZC crystal was found to show Curie phase transition at 151 °C. TG/DTA confirmed the melting point that was found to be 443 °C. The value of piezoelectric charge coefficient (d{sub 33}) for KZC crystal was found to be 32 pC/N demonstrating their applicability in transducers and piezoelectric devices. Ferroelectric P-E loop for the grown crystal was traced at room temperature and the intrinsic polarization obtained by PUND measurement was found to be 0.1398 μC/cm{sup 2} indicating its applicability in switching devices. The energy band gap for KZC single crystal was found to be 6.13 eV. Vickers micro-hardness test revealed soft nature of KZC single crystals. - Highlights: • Large sized K{sub 2}ZnCl{sub 4} (KZC) single crystal was grown by Czochralski technique. • It possesses high Curie temperature as 151 °C. • d{sub 33} coefficient was found to be 32 pC/N. • Intrinsic polarization measured by PUND. • Its direct band gap energy was calculated to be 6.13 eV.

  19. Pseudo single crystal, direct-band-gap Ge{sub 0.89}Sn{sub 0.11} on amorphous dielectric layers towards monolithic 3D photonic integration

    Energy Technology Data Exchange (ETDEWEB)

    Li, Haofeng; Brouillet, Jeremy; Wang, Xiaoxin; Liu, Jifeng, E-mail: Jifeng.Liu@dartmouth.edu [Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755 (United States)

    2014-11-17

    We demonstrate pseudo single crystal, direct-band-gap Ge{sub 0.89}Sn{sub 0.11} crystallized on amorphous layers at <450 °C towards 3D Si photonic integration. We developed two approaches to seed the lateral single crystal growth: (1) utilize the Gibbs-Thomson eutectic temperature depression at the tip of an amorphous GeSn nanotaper for selective nucleation; (2) laser-induced nucleation at one end of a GeSn strip. Either way, the crystallized Ge{sub 0.89}Sn{sub 0.11} is dominated by a single grain >18 μm long that forms optoelectronically benign twin boundaries with others grains. These pseudo single crystal, direct-band-gap Ge{sub 0.89}Sn{sub 0.11} patterns are suitable for monolithic 3D integration of active photonic devices on Si.

  20. How are base excision DNA repair pathways deployed in vivo? [version 1; referees: 4 approved

    Directory of Open Access Journals (Sweden)

    Upasna Thapar

    2017-03-01

    Full Text Available Since the discovery of the base excision repair (BER system for DNA more than 40 years ago, new branches of the pathway have been revealed at the biochemical level by in vitro studies. Largely for technical reasons, however, the confirmation of these subpathways in vivo has been elusive. We review methods that have been used to explore BER in mammalian cells, indicate where there are important knowledge gaps to fill, and suggest a way to address them.

  1. Multi-locus genotyping of bottom fermenting yeasts by single nucleotide polymorphisms indicative of brewing characteristics.

    Science.gov (United States)

    Ikushima, Shigehito; Tateishi, Yoshiyuki; Kanai, Keiko; Shimada, Emiko; Tanaka, Misa; Ishiguro, Tatsuji; Mizutani, Satoru; Kobayashi, Osamu

    2012-04-01

    Yeast plays a capital role in brewing fermentation and has a direct impact on flavor and aroma. For the evaluation of competent brewing strains during quality control or development of novel strains it is standard practice to perform fermentation tests, which are costly and time-consuming. Here, we have categorized DNA markers which enable to distinguish and to screen brewing strains more efficiently than ever before. Sequence analysis at 289 loci in the genomes of six bottom fermenting Saccharomyces pastorianus strains revealed that 30 loci contained single nucleotide polymorphisms (SNPs). By determining the nucleotide sequences at the SNP-loci in 26 other S. pastorianus strains and 20 strains of the top fermenting yeast Saccharomyces cerevisiae, almost all these strains could be discriminated solely on the basis of the SNPs. By comparing the fermentative phenotypes of these strains we found that some DNA markers showed a strong association with brewing characteristics, such as the production of ethyl acetate and hydrogen sulphide (H2S). Therefore, the DNA markers we identified will facilitate quality control and the efficient development of brewing yeast strains. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  2. Differential role of base excision repair proteins in mediating cisplatin cytotoxicity.

    Science.gov (United States)

    Sawant, Akshada; Floyd, Ashley M; Dangeti, Mohan; Lei, Wen; Sobol, Robert W; Patrick, Steve M

    2017-03-01

    Interstrand crosslinks (ICLs) are covalent lesions formed by cisplatin. The mechanism for the processing and removal of ICLs by DNA repair proteins involves nucleotide excision repair (NER), homologous recombination (HR) and fanconi anemia (FA) pathways. In this report, we monitored the processing of a flanking uracil adjacent to a cisplatin ICL by the proteins involved in the base excision repair (BER) pathway. Using a combination of extracts, purified proteins, inhibitors, functional assays and cell culture studies, we determined the specific BER proteins required for processing a DNA substrate with a uracil adjacent to a cisplatin ICL. Uracil DNA glycosylase (UNG) is the primary glycosylase responsible for the removal of uracils adjacent to cisplatin ICLs, whereas other uracil glycosylases can process uracils in the context of undamaged DNA. Repair of the uracil adjacent to cisplatin ICLs proceeds through the classical BER pathway, highlighting the importance of specific proteins in this redundant pathway. Removal of uracil is followed by the generation of an abasic site and subsequent cleavage by AP endonuclease 1 (APE1). Inhibition of either the repair or redox domain of APE1 gives rise to cisplatin resistance. Inhibition of the lyase domain of Polymerase β (Polβ) does not influence cisplatin cytotoxicity. In addition, lack of XRCC1 leads to increased DNA damage and results in increased cisplatin cytotoxicity. Our results indicate that BER activation at cisplatin ICLs influences crosslink repair and modulates cisplatin cytotoxicity via specific UNG, APE1 and Polβ polymerase functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Sound velocity and attenuation in single-crystal YBa2Cu3O/sub 7-//sub δ/

    International Nuclear Information System (INIS)

    Shi, X.D.; Yu, R.C.; Wang, Z.Z.; Ong, N.P.; Chaikin, P.M.

    1989-01-01

    We have used a modified vibrating reed technique to measure the temperature dependence of the sound velocity and attenuation for modes corresponding to the Young's modulus and c/sub 14/ shear modulus of single crystals of YBa 2 Cu 3 O/sub 7-//sub δ/. The Young's sound velocity shows a tremendous softening during the superconducting transition: a smeared discontinuity of as high as 190 ppm. Below the transition, the temperature dependences of both sound velocities harden considerably. The discontinuities of the sound velocities and their temperature derivatives at T/sub c/ are related to the specific-heat jump at the superconducting transition

  4. Single nucleotide polymorphisms (SNPs in coding regions of canine dopamine- and serotonin-related genes

    Directory of Open Access Journals (Sweden)

    Lingaas Frode

    2008-01-01

    Full Text Available Abstract Background Polymorphism in genes of regulating enzymes, transporters and receptors of the neurotransmitters of the central nervous system have been associated with altered behaviour, and single nucleotide polymorphisms (SNPs represent the most frequent type of genetic variation. The serotonin and dopamine signalling systems have a central influence on different behavioural phenotypes, both of invertebrates and vertebrates, and this study was undertaken in order to explore genetic variation that may be associated with variation in behaviour. Results Single nucleotide polymorphisms in canine genes related to behaviour were identified by individually sequencing eight dogs (Canis familiaris of different breeds. Eighteen genes from the dopamine and the serotonin systems were screened, revealing 34 SNPs distributed in 14 of the 18 selected genes. A total of 24,895 bp coding sequence was sequenced yielding an average frequency of one SNP per 732 bp (1/732. A total of 11 non-synonymous SNPs (nsSNPs, which may be involved in alteration of protein function, were detected. Of these 11 nsSNPs, six resulted in a substitution of amino acid residue with concomitant change in structural parameters. Conclusion We have identified a number of coding SNPs in behaviour-related genes, several of which change the amino acids of the proteins. Some of the canine SNPs exist in codons that are evolutionary conserved between five compared species, and predictions indicate that they may have a functional effect on the protein. The reported coding SNP frequency of the studied genes falls within the range of SNP frequencies reported earlier in the dog and other mammalian species. Novel SNPs are presented and the results show a significant genetic variation in expressed sequences in this group of genes. The results can contribute to an improved understanding of the genetics of behaviour.

  5. Giant volume magnetostriction in the Y{sub 2}Fe{sub 17} single crystal at room temperature

    Energy Technology Data Exchange (ETDEWEB)

    Nikitin, S. A., E-mail: nikitin@phys.msu.ru; Pankratov, N. Yu.; Smarzhevskaya, A. I.; Politova, G. A. [Physics Faculty, Lomonosov Moscow State University, Moscow 119992 (Russian Federation); Pastushenkov, Yu. G., E-mail: yupast@mail.ru; Skokov, K. P. [Physics Faculty, Tver State University, 170100 Tver (Russian Federation); Moral, A. del [Laboratorio de Magnetismo de Slidos, Departamento de Fisica de Materia Condensada and Instituto de Ciencia de Materiales de Aragn, Facultad de Ciencias, Universidad de Zaragoza-C.S.I.C, E-50009 Zaragoza (Spain)

    2015-05-21

    An investigation of the Y{sub 2}Fe{sub 17} compound belonging to the class of intermetallic alloys of rare-earth and 3d-transition metals is presented. The magnetization, magnetostriction, and thermal expansion of the Y{sub 2}Fe{sub 17} single crystal were studied. The forced magnetostriction and magnetostriction constants were investigated in the temperature range of the magnetic ordering close to the room temperature. The giant field induced volume magnetostriction was discovered in the room temperature region in the magnetic field up to 1.2 T. The contributions of both anisotropic single-ion and isotropic pair exchange interactions to the volume magnetostriction and magnetostriction constants were determined. The experimental results were interpreted within the framework of the Standard Theory of Magnetostriction and the Landau thermodynamic theory. It was found out that the giant values of the volume magnetostriction were caused by the strong dependence of the 3d-electron Coulomb charge repulsion on the deformations and width of the 3d-electron energy band.

  6. TNF/TNFR{sub 1} pathway and endoplasmic reticulum stress are involved in ofloxacin-induced apoptosis of juvenile canine chondrocytes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Fu-Tao; Ding, Yi; Shah, Zahir; Xing, Dan; Gao, Yuan; Liu, Dong Ming; Ding, Ming-Xing, E-mail: dmx@mail.hzau.edu.cn

    2014-04-15

    Background and purpose: Quinolones cause obvious cartilaginous lesions in juvenile animals by chondrocyte apoptosis, which results in the restriction of their use in pediatric and adolescent patients. Studies showed that chondrocytes can be induced to produce TNFα, and the cisternae of the endoplasmic reticulum in quinolone-treated chondrocytes become dilated. We investigated whether TNF/TNFR{sub 1} pathway and endoplasmic reticulum stress (ERs) are involved in ofloxacin (a typical quinolone)-induced apoptosis of juvenile canine chondrocytes. Experimental approach: Canine juvenile chondrocytes were treated with ofloxacin. Cell survival and apoptosis rates were determined with MTT method and flow cytometry, respectively. The gene expression levels of the related signaling molecules (TNFα, TNFR{sub 1}, TRADD, FADD and caspase-8) in death receptor pathways and main apoptosis-related molecules (calpain, caspase-12, GADD153 and GRP78) in ERs were measured by qRT-PCR. The gene expression of TNFR{sub 1} was suppressed with its siRNA. The protein levels of TNFα, TNFR{sub 1} and caspase-12 were assayed using Western blotting. Key results: The survival rates decreased while apoptosis rates increased after the chondrocytes were treated with ofloxacin. The mRNA levels of the measured apoptosis-related molecules in death receptor pathways and ERs, and the protein levels of TNFα, TNFR{sub 1} and caspase-12 increased after the chondrocytes were exposed to ofloxacin. The downregulated mRNA expressions of TNFR{sub 1}, Caspase-8 and TRADD, and the decreased apoptosis rates of the ofloxacin-treated chondrocytes occurred after TNFR{sub 1}–siRNA interference. Conclusions and implications: Ofloxacin-induced chondrocyte apoptosis in a time- and concentration-dependent fashion. TNF/TNFR{sub 1} pathway and ERs are involved in ofloxacin-induced apoptosis of juvenile canine chondrocytes in the early stage. - Highlights: • Chondrocyte apoptosis is induced by ofloxacin in a time- and

  7. Single crystalline Er{sub 2}O{sub 3}:sapphire films as potentially high-gain amplifiers at telecommunication wavelength

    Energy Technology Data Exchange (ETDEWEB)

    Kuznetsov, A. S.; Sadofev, S.; Schäfer, P.; Kalusniak, S.; Henneberger, F., E-mail: fh@physik.hu-berlin.de [Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, D-12489 Berlin (Germany)

    2014-11-10

    Single crystalline thin films of Er{sub 2}O{sub 3}, demonstrating efficient 1.5 μm luminescence of Er{sup 3+} at room temperature were grown on Al{sub 2}O{sub 3} substrate by molecular beam epitaxy. The absorption coefficient at 1.536 μm was found to reach 270 cm{sup −1} translating in a maximal possible gain of 1390 dBcm{sup −1}. In conjunction with the 10% higher refractive index as compared to Al{sub 2}O{sub 3}, this opens the possibility to use Er{sub 2}O{sub 3}:sapphire films as short-length waveguide amplifiers in telecommunication.

  8. Determination of the hydrogen positions in the novel barium boroarsenate Ba[B{sub 2}As{sub 2}O{sub 8}(OH){sub 2}] by combined single crystal X-ray and powder neutron investigations

    Energy Technology Data Exchange (ETDEWEB)

    Lieb, Alexandra [School of Chemistry, University of Southampton (United Kingdom); Fakultaet fuer Verfahrens- und Systemtechnik, Lehrstuhl fuer Technische Chemie, Otto-von-Guericke-Universitaet, Magdeburg (Germany); Weller, Mark T. [School of Chemistry, University of Southampton (United Kingdom); Department of Chemistry, University of Bath (United Kingdom)

    2017-11-17

    The boroarsenate Ba[B{sub 2}As{sub 2}O{sub 8}(OH){sub 2}] was obtained by the reaction of NH{sub 4}H{sub 2}AsO{sub 4}, B(OH){sub 3} and BaBr{sub 2}.2H{sub 2}O in the melt. Ba[B{sub 2}As{sub 2}O{sub 8}(OH){sub 2}] was obtained as thin colorless needles, together with spherical crystals of BAsO{sub 4} as by-product, grown on a pellet of Ba[BAsO{sub 5}]. The products could be separated mechanically. For neutron scattering experiments a sample was prepared with {sup 11}B(OH){sub 3} as a starting material. The crystal structure of Ba[B{sub 2}As{sub 2}O{sub 8}(OH){sub 2}] was determined by single-crystal X-ray diffraction and exhibits a layer structure with an unprecedented layer topology. The exact positions of the hydrogen atoms were determined using combined single-crystal X-ray and powder neutron diffraction investigations. Ba[B{sub 2}As{sub 2}O{sub 8}(OH){sub 2}] was further characterized by IR spectroscopy and EDX analysis. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Hard X-ray MCD in GdNi/sub 5/ and TbNi/sub 5/ single crystals

    CERN Document Server

    Galera, R M

    1999-01-01

    XMCD experiments have been performed at the R L/sub 2,3/ and Ni K- edges on magnetically saturated single crystals of GdNi/sub 5/ and Tb Ni/sub 5/ ferromagnetic compounds. The spectra present huge and well structured dichroic $9 signals at both the R L/sub 2,3/ and the Ni K- edges. Structures from the quadrupolar (2p to 4f) transitions are clearly observed at the R L/sub 2,3/-edges. Though Ni is not magnetic, large intensities, up to 0.4, are measured at the $9 Ni K- edge. The Ni K-edge XMCD shows a three-peak structure which intensities dependent on the rare earth. (7 refs).

  10. Determination of NAD+ and NADH level in a Single Cell Under H<sub>2sub>O>2sub> Stress by Capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Xi, Wenjun [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    A capillary electrophoresis (CE) method is developed to determine both NAD+ and NADH levels in a single cell, based on an enzymatic cycling reaction. The detection limit can reach down to 0.2 amol NAD+ and 1 amol NADH on a home-made CE-LIF setup. The method showed good reproducibility and specificity. After an intact cell was injected into the inlet of a capillary and lysed using a Tesla coil, intracellular NAD+ and NADH were separated, incubated with the cycling buffer, and quantified by the amount of fluorescent product generated. NADH and NAD+ levels of single cells of three cell lines and primary astrocyte culture were determined using this method. Comparing cellular NAD+ and NADH levels with and without exposure to oxidative stress induced by H<sub>2sub>O>2sub>, it was found that H9c2 cells respond to the stress by reducing both cellular NAD+ and NADH levels, while astrocytes respond by increasing cellular NADH/NAD+ ratio.

  11. Electrical and photoelectric properties of PbGa{sub 2}Se{sub 4} single crystals; Ehlektricheskie i fotoehlektricheskie svojstva monokristalla PbGa{sub 2}Se{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Tagiev, B G; Tagiev, O B; Dzhabbarov, R B; Musaeva, N N [AN Azerbajdzhana, Inst. Fiziki, Baku (Azerbaijan)

    1999-01-01

    Thermal dependence of dark current spectral distribution of photocurrent and temperature quenching of photocurrent of PbGa{sub 2}Se{sub 4} single crystals are investigated. Concentrations and mobilities of free charge carriers, concentrations and activation energies of gaps, values of Fermi level and forbidden zone width are calculated.

  12. Raman spectroscopic studies of Nd{sub 0.75}Sm{sub 0.25}GaO{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Nithya, R., E-mail: nithya@igcar.gov.in; Ravindran, T. R. [Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam-603102, TN (India); Daniel, D. J. [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam-603110, TN (India)

    2015-06-24

    Single crystals of Nd{sub 1-x}Sm{sub x}GaO{sub 3} (x= 0 and 0.25) were grown by a four mirror IR image furnace using floating zone technique. The crystals are characterized by X-ray diffraction and Raman spectroscopic measurements. NGO adopts orthorhombic structure with Pbnm symmetry and samarium substituted compound also exhibited the same structure as that of the pristine compound without secondary phases. Polarized Raman spectra are measured at ambient temperature in a back scattering geometry. Spectra exhibit low intensity first-order Raman bands. In addition, several high intensity second-order Raman bands have been observed in the frequency range 2000 to 4000 cm{sup −1}.

  13. Simultaneous Detection of Both Single Nucleotide Variations and Copy Number Alterations by Next-Generation Sequencing in Gorlin Syndrome.

    Directory of Open Access Journals (Sweden)

    Kei-ichi Morita

    Full Text Available Gorlin syndrome (GS is an autosomal dominant disorder that predisposes affected individuals to developmental defects and tumorigenesis, and caused mainly by heterozygous germline PTCH1 mutations. Despite exhaustive analysis, PTCH1 mutations are often unidentifiable in some patients; the failure to detect mutations is presumably because of mutations occurred in other causative genes or outside of analyzed regions of PTCH1, or copy number alterations (CNAs. In this study, we subjected a cohort of GS-affected individuals from six unrelated families to next-generation sequencing (NGS analysis for the combined screening of causative alterations in Hedgehog signaling pathway-related genes. Specific single nucleotide variations (SNVs of PTCH1 causing inferred amino acid changes were identified in four families (seven affected individuals, whereas CNAs within or around PTCH1 were found in two families in whom possible causative SNVs were not detected. Through a targeted resequencing of all coding exons, as well as simultaneous evaluation of copy number status using the alignment map files obtained via NGS, we found that GS phenotypes could be explained by PTCH1 mutations or deletions in all affected patients. Because it is advisable to evaluate CNAs of candidate causative genes in point mutation-negative cases, NGS methodology appears to be useful for improving molecular diagnosis through the simultaneous detection of both SNVs and CNAs in the targeted genes/regions.

  14. Simultaneous Detection of Both Single Nucleotide Variations and Copy Number Alterations by Next-Generation Sequencing in Gorlin Syndrome.

    Science.gov (United States)

    Morita, Kei-ichi; Naruto, Takuya; Tanimoto, Kousuke; Yasukawa, Chisato; Oikawa, Yu; Masuda, Kiyoshi; Imoto, Issei; Inazawa, Johji; Omura, Ken; Harada, Hiroyuki

    2015-01-01

    Gorlin syndrome (GS) is an autosomal dominant disorder that predisposes affected individuals to developmental defects and tumorigenesis, and caused mainly by heterozygous germline PTCH1 mutations. Despite exhaustive analysis, PTCH1 mutations are often unidentifiable in some patients; the failure to detect mutations is presumably because of mutations occurred in other causative genes or outside of analyzed regions of PTCH1, or copy number alterations (CNAs). In this study, we subjected a cohort of GS-affected individuals from six unrelated families to next-generation sequencing (NGS) analysis for the combined screening of causative alterations in Hedgehog signaling pathway-related genes. Specific single nucleotide variations (SNVs) of PTCH1 causing inferred amino acid changes were identified in four families (seven affected individuals), whereas CNAs within or around PTCH1 were found in two families in whom possible causative SNVs were not detected. Through a targeted resequencing of all coding exons, as well as simultaneous evaluation of copy number status using the alignment map files obtained via NGS, we found that GS phenotypes could be explained by PTCH1 mutations or deletions in all affected patients. Because it is advisable to evaluate CNAs of candidate causative genes in point mutation-negative cases, NGS methodology appears to be useful for improving molecular diagnosis through the simultaneous detection of both SNVs and CNAs in the targeted genes/regions.

  15. DivStat: a user-friendly tool for single nucleotide polymorphism analysis of genomic diversity.

    Directory of Open Access Journals (Sweden)

    Inês Soares

    Full Text Available Recent developments have led to an enormous increase of publicly available large genomic data, including complete genomes. The 1000 Genomes Project was a major contributor, releasing the results of sequencing a large number of individual genomes, and allowing for a myriad of large scale studies on human genetic variation. However, the tools currently available are insufficient when the goal concerns some analyses of data sets encompassing more than hundreds of base pairs and when considering haplotype sequences of single nucleotide polymorphisms (SNPs. Here, we present a new and potent tool to deal with large data sets allowing the computation of a variety of summary statistics of population genetic data, increasing the speed of data analysis.

  16. Analysis of healthy cohorts for single nucleotide polymorphisms in C1q gene cluster

    Directory of Open Access Journals (Sweden)

    MARIA A. RADANOVA

    2015-12-01

    Full Text Available C1q is the first component of the classical pathway of complement activation. The coding region for C1q is localized on chromosome 1p34.1–36.3. Mutations or single nucleotide polymorphisms (SNPs in C1q gene cluster can cause developing of Systemic lupus erythematosus (SLE because of C1q deficiency or other unknown reason. We selected five SNPs located in 7.121 kbp region on chromosome 1, which were previously associated with SLE and/or low C1q level, but not causing C1q deficiency and analyzed them in terms of allele frequencies and genotype distribution in comparison with Hispanic, Asian, African and other Caucasian cohorts. These SNPs were: rs587585, rs292001, rs172378, rs294179 and rs631090. One hundred eighty five healthy Bulgarian volunteers were genotyped for the selected five C1q SNPs by quantative real-time PCR methods. International HapMap Project has been used for information about genotype distribution and allele frequencies of the five SNPs in, Hispanics, Asians, Africans and others Caucasian cohorts. Bulgarian healthy volunteers and another pooled Caucasian cohort had similar frequencies of genotypes and alleles of rs587585, rs292001, rs294179 and rs631090 SNPs. Nevertheless, genotype AA of rs172378 was significantly overrepresented in Bulgarians when compared to other healthy Caucasians from USA and UK (60% vs 31%. Genotype distribution of rs172378 in Bulgarians was similar to Greek-Cyriot Caucasians. For all Caucasians the major allele of rs172378 was A. This is the first study analyzing the allele frequencies and genotype distribution of C1q gene cluster SNPs in Bulgarian healthy population.

  17. Ferroelectric InMnO{sub 3}: Growth of single crystals, structure and high-temperature phase transitions

    Energy Technology Data Exchange (ETDEWEB)

    Bekheet, Maged F., E-mail: maged.bekheet@ceramics.tu-berlin.de [Fachbereich Material‐ und Geowissenschaften, Technische Universität Darmstadt, Alarich-Weiss-Straße 2, 64287 Darmstadt (Germany); Fachgebiet Keramische Werkstoffe / Chair of Advanced Ceramic Materials, Institut für Werkstoffwissenschaften und -technologien, Technische Universität Berlin, Hardenbergstraße 40, 10623 Berlin (Germany); Svoboda, Ingrid; Liu, Na [Fachbereich Material‐ und Geowissenschaften, Technische Universität Darmstadt, Alarich-Weiss-Straße 2, 64287 Darmstadt (Germany); Bayarjargal, Lkhamsuren [Institut für Geowissenschaften, Goethe-Universität, Altenhöferallee 1, d-60438 Frankfurt a.M. (Germany); Irran, Elisabeth [Institut für Chemie, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin (Germany); Dietz, Christian; Stark, Robert W.; Riedel, Ralf [Fachbereich Material‐ und Geowissenschaften, Technische Universität Darmstadt, Alarich-Weiss-Straße 2, 64287 Darmstadt (Germany); Gurlo, Aleksander [Fachgebiet Keramische Werkstoffe / Chair of Advanced Ceramic Materials, Institut für Werkstoffwissenschaften und -technologien, Technische Universität Berlin, Hardenbergstraße 40, 10623 Berlin (Germany)

    2016-09-15

    To understand the origin of the ferroelectricity in InMnO{sub 3}, single crystals with average size of 1 mm were grown in PbF{sub 2} flux at 950 °C. The results of single crystal X-ray diffraction, second harmonic generation and piezoresponse force microscopy studies of high-quality InMnO{sub 3} single crystals reveal that the room-temperature state in this material is ferroelectric with P6{sub 3}cm symmetry. The polar InMnO{sub 3} specimen undergoes a reversible phase transition from non-centrosymmetric P6{sub 3}cm structure to a centrosymmetric P6{sub 3}/mmc structure at 700 °C as confirmed by the in situ high-temperature Raman spectroscopic and synchrotron X-ray diffraction experiments. - Graphical abstract: Piezoresponse fore microscopy (PFM) studies of high quality InMnO{sub 3} single crystal revealed that the room-temperature state of this material is ferroelectric with a clear cloverleaf pattern corresponding to six antiphase ferroelectric domains with alternating polarization ±P{sub z}. Display Omitted - Highlights: • InMnO{sub 3} single crystals with average size of 1 mm were grown in PbF{sub 2} flux at 950 °C. • The room-temperature state of InMnO{sub 3} is ferroelectric with polar P6{sub 3}cm structure. • PolarInMnO{sub 3} reversibly transforms to a centrosymmetric P6{sub 3}/mmc structure above 700 °C.

  18. Common genetic variations in cell cycle and DNA repair pathways associated with pediatric brain tumor susceptibility

    DEFF Research Database (Denmark)

    Fahmideh, Maral Adel; Lavebratt, Catharina; Schüz, Joachim

    2016-01-01

    Knowledge on the role of genetic polymorphisms in the etiology of pediatric brain tumors (PBTs) is limited. Therefore, we investigated the association between single nucleotide polymorphisms (SNPs), identified by candidate gene-association studies on adult brain tumors, and PBT risk. The study is...... cycle and DNA repair pathways variations associated with susceptibility to adult brain tumors also seem to be associated with PBT risk, suggesting pediatric and adult brain tumors might share similar etiological pathways....

  19. Synthesis, structural, X-ray photoelectron spectroscopy (XPS) studies and IR induced anisotropy of Tl{sub 4}HgI{sub 6} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Parasyuk, O.V. [Department of Inorganic and Physical Chemistry, Lesya Ukrainka Eastern European National University, Voli Ave. 13, Lutsk, 43025 (Ukraine); Khyzhun, O.Y. [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky St., 03142, Kyiv (Ukraine); Piasecki, M. [Institute of Physics, J. Dlugosz University Częstochowa, Armii Krajowej 13/15, Częstochowa (Poland); Kityk, I.V., E-mail: iwank74@gmail.com [Electrical Engineering Department, Czestochowa University Technology, Armii Krajowej 17, PL-42-217, Czestochowa (Poland); Lakshminarayana, G. [Wireless and Photonic Networks Research Centre, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor (Malaysia); Luzhnyi, I. [Frantsevych Institute for Problems of Materials Science, National Academy of Sciences of Ukraine, 3 Krzhyzhanivsky St., 03142, Kyiv (Ukraine); Fochuk, P.M. [Yuriy Fed’kovych Chernivtsi National University, 2 Kotziubynskoho Str., 58012, Chernivtsi (Ukraine); Fedorchuk, A.O. [Department of Inorganic and Organic Chemistry, Lviv National University of Veterinary Medicine and Biotechnologies, Pekarska Street 50, 79010, Lviv (Ukraine); Levkovets, S.I.; Yurchenko, O.M.; Piskach, L.V. [Department of Inorganic and Physical Chemistry, Lesya Ukrainka Eastern European National University, Voli Ave. 13, Lutsk, 43025 (Ukraine)

    2017-02-01

    In the present work, we report on the synthesis and structural properties including X-ray protoelectron spectroscopy (XPS) analysis of Tl{sub 4}HgI{sub 6} crystals that were grown by Bridgman-Stockbarger method up to 80 mm in length and 18 mm in diameter. The existence of the ternary compound Tl{sub 4}HgI{sub 6} that melts incongruently at 641 K was confirmed. Phase equilibria and structural properties for the TlI–HgI{sub 2} system were investigated by differential thermal analysis (DTA) and X-ray diffraction (XRD) methods. X-ray photoelectron spectra were measured for both pristine and Ar{sup +} ion-bombarded Tl{sub 4}HgI{sub 6} single crystal surfaces. The data reveal that the Tl{sub 4}HgI{sub 6} single crystal is sensitive with respect to Ar{sup +} ion-bombardment as 3.0 keV Ar{sup +} irradiation over 5 min at an ion current density 14 μA/cm{sup 2} induces changes to the elemental stoichiometry of the Tl{sub 4}HgI{sub 6} surface, leading to a decrease of the mercury content in the topmost surface layers. X-ray photoelectron spectroscopy (XPS) measurements indicate very low hygroscopic nature of the Tl{sub 4}HgI{sub 6} single crystal surface. The IR coherent bicolor laser treatment at wavelengths 10.6/5.3 μm has shown an occurrence of anisotropy at wavelengths 1540 nm of Er:glass laser. This may open the applications of Tl{sub 4}HgI{sub 6} as a material for IR laser triggering. - Highlights: • Phase diagram of the HgI{sub 2}–TlI system was built. • Tl{sub 4}HgI{sub 6} single crystals were grown by Bridgman Stockbarger method. • XRD, XPS analysis was done. • Ir induced anisotropy was established. • The compounds may be proposed as Ir laser operated polarizers.

  20. The crystal structure and luminescence quenching of poly- and single-crystalline KYW{sub 2}O{sub 8}:Tb{sup 3+}

    Energy Technology Data Exchange (ETDEWEB)

    Schwung, Sebastian [Fachbereich Chemieingenieurwesen, Fachhochschule Münster, Stegerwaldstraße 39, 48565 Steinfurt (Germany); Rytz, Daniel, E-mail: rytz@fee-io.de [Forschungsinstitut für mineralische und metallische Werkstoffe-Edelsteine/ Edelmetalle-GmbH (FEE), Struthstraße 2, 55743 Idar-Oberstein (Germany); Heying, Birgit; Rodewald, Ute Ch.; Niehaus, Oliver [Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstrasse 30 48149 Münster (Germany); Enseling, David [Fachbereich Chemieingenieurwesen, Fachhochschule Münster, Stegerwaldstraße 39, 48565 Steinfurt (Germany); Jüstel, Thomas, E-mail: tj@fh-muenster.de [Fachbereich Chemieingenieurwesen, Fachhochschule Münster, Stegerwaldstraße 39, 48565 Steinfurt (Germany); Pöttgen, Rainer, E-mail: pottgen@uni-muenster.de [Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstrasse 30 48149 Münster (Germany)

    2015-10-15

    Terbium-substituted KYW{sub 2}O{sub 8} single crystals of high optical quality were grown by the top seeded solution growth technique. The degree of yttrium–terbium mixed occupancy was determined for two samples through structure refinements on the basis of single crystal X-ray diffractometer data. Temperature dependent magnetic susceptibility data underline the paramagnetic nature of terbium doped crystals. No magnetic ordering is evident down to 2 K. Luminescence measurements yield the typical excitation and emission spectra as expected for Tb{sup 3+} activated materials. The decay time of Tb{sup 3+} decreases linearly with the Tb{sup 3+} concentration, while the excess of thermal quenching does not change significantly. At about 405 K the decay time is reduced by roughly 50% relative to the low-temperature value, both for the powders as for the single crystals. - Highlights: • Single crystalline and powder series of K(Y,Tb)W{sub 2}O{sub 8.} • Refined XRD data of high quality crystals. • Linear decrease of the decay time with Tb{sup 3+} content.

  1. Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

    Science.gov (United States)

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

    2017-09-01

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

  2. Nucleotide Selectivity in Abiotic RNA Polymerization Reactions.

    Science.gov (United States)

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

    2017-09-01

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

  3. Assessing patterns of hybridization between North Atlantic eels using diagnostic single-nucleotide polymorphisms

    DEFF Research Database (Denmark)

    Pujolar, José Martin; Jacobsen, M.W.; Als, Thomas Damm

    2014-01-01

    The two North Atlantic eel species, the European eel (Anguilla anguilla) and the American eel (Anguilla rostrata), spawn in partial sympatry in the Sargasso Sea, providing ample opportunity to interbreed. In this study, we used a RAD (Restriction site Associated DNA) sequencing approach to identify...... species-specific diagnostic single-nucleotide polymorphisms (SNPs) and design a low-density array that combined with screening of a diagnostic mitochondrial DNA marker. Eels from Iceland (N=159) and from the neighboring Faroe Islands (N=29) were genotyped, along with 94 larvae (49 European and 45 American...... eel male crosses, backcrosses were also detected, including a first-generation backcross (F1 hybrid × pure European eel) and three individuals identified as second-generation backcrosses originating from American eel × F1 hybrid backcrosses interbreeding with pure European eels. In comparison...

  4. The single crystal structure determination of Ln{sub 6}MnSb{sub 15} (Ln=La, Ce), Ln{sub 6}Mn{sub 1-x}Zn{sub x}Sb{sub 15} (x∝0.5), and Ln{sub 6}ZnSb{sub 15} (Ln=La-Pr)

    Energy Technology Data Exchange (ETDEWEB)

    Benavides, Katherine A.; McCandless, Gregory T.; Chan, Julia Y. [Texas Univ., Dallas, Richardson, TX (United States). Dept. of Chemistry and Biochemistry

    2017-09-01

    Single crystals of Ln{sub 6}MnSb{sub 15} (Ln=La, Ce), Ln{sub 6}Mn{sub 1-x}Zn{sub x}Sb{sub 15} (x∝0.5), and Ln{sub 6}ZnSb{sub 15} (Ln=La-Pr) have been successfully grown and the compounds adopt the orthorhombic Ln{sub 6}MnSb{sub 15} structure type (space group Immm), with a∝4.3 Aa, b∝15 Aa, and c∝19 Aa. This structure is comprised of antimony nets and antimony ribbons which exhibit positional disorder at connecting points between antimony substructures, in addition to two partially occupied transition metal sites. The unit cell volumes of the La analogs displayed a systematic decrease upon Zn substitution. However, for the Ce{sub 6}Mn{sub 1-x}Zn{sub x}Sb{sub 15} and Pr{sub 6}Mn{sub 1-x}Zn{sub x}Sb{sub 15} (x∝0.5), the volumes deviate from linearity as observed in the parent compounds.

  5. Electron paramagnetic resonance spectral study of [Mn(acs){sub 2}(2–pic){sub 2}(H{sub 2}O){sub 2}] single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kocakoç, Mehpeyker, E-mail: mkocakoc@cu.edu.tr [Çukurova University (Turkey); Tapramaz, Recep, E-mail: recept@omu.edu.tr [Ondokuz Mayıs University (Turkey)

    2016-03-25

    Acesulfame potassium salt is a synthetic and non-caloric sweetener. It is also important chemically for its capability of being ligand in coordination compounds, because it can bind over Nitrogen and Oxygen atoms of carbonyl and sulfonyl groups and ring oxygen. Some acesulfame containing transition metal ion complexes with mixed ligands exhibit solvato and thermo chromic properties and these properties make them physically important. In this work single crystals of Mn{sup +2} ion complex with mixed ligand, [Mn(acs){sub 2}(2-pic){sub 2}(H{sub 2}O){sub 2}], was studied with electron paramagnetic resonance (EPR) spectroscopy. EPR parameters were determined. Zero field splitting parameters indicated that the complex was highly symmetric. Variable temperature studies showed no detectable chance in spectra.

  6. Unusual magnetic properties of UGa{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kaczorowski, D.; Klamut, P.W.; Czopnik, A.; Jezowski, A. [Polska Akademia Nauk, Wroclaw (Poland). Inst. Niskich Temperatur i Badan Strukturalnych

    1998-01-01

    The magnetic behaviour of single-crystalline UGa{sub 3} has been studied by means of DC- and AC-magnetic susceptibility and thermal conductivity measurements. As many as three pronounced singularities have been found in both, the {chi}(T) and {kappa}(T) variations. The features at T{sub N} = 65 K are associated with an antiferromagnetic phase transition while those at T{sub 1} = 40 K and T{sub 2} = 8 K have an unknown origin. At low temperatures a significant diamagnetic response is observed in {chi}`(T) accompanied by a rapid rise in {chi}{sup ``}(T). This behaviour of the AC-susceptibility is strongly dependent on the frequency of the alternating magnetic field and on the strength of the external steady magnetic field. (orig.) 7 refs.

  7. Single-session Gamma Knife radiosurgery for optic pathway/hypothalamic gliomas.

    Science.gov (United States)

    El-Shehaby, Amr M N; Reda, Wael A; Abdel Karim, Khaled M; Emad Eldin, Reem M; Nabeel, Ahmed M

    2016-12-01

    OBJECTIVE Because of their critical and central location, it is deemed necessary to fractionate when considering irradiating optic pathway/hypothalamic gliomas. Stereotactic fractionated radiotherapy is considered safer when dealing with gliomas in this location. In this study, the safety and efficacy of single-session stereotactic radiosurgery for optic pathway/hypothalamic gliomas were reviewed. METHODS Between December 2004 and June 2014, 22 patients with optic pathway/hypothalamic gliomas were treated by single-session Gamma Knife radiosurgery. Twenty patients were available for follow-up for a minimum of 1 year after treatment. The patients were 5 to 43 years (median 16 years) of age. The tumor volume was 0.15 to 18.2 cm 3 (median 3.1 cm 3 ). The prescription dose ranged from 8 to 14 Gy (median 11.5 Gy). RESULTS The mean follow-up period was 43 months. Five tumors involved the optic nerve only, and 15 tumors involved the chiasm/hypothalamus. Two patients died during the follow-up period. The tumors shrank in 12 cases, remained stable in 6 cases, and progressed in 2 cases, thereby making the tumor control rate 90%. Vision remained stable in 12 cases, improved in 6 cases, and worsened in 2 cases in which there was tumor progression. Progression-free survival was 83% at 3 years. CONCLUSIONS The initial results indicate that single-session Gamma Knife radiosurgery is a safe and effective treatment option for optic pathway/hypothalamic gliomas.

  8. Parallel pathways of ethoxylated alcohol biodegradation under aerobic conditions

    Energy Technology Data Exchange (ETDEWEB)

    Zembrzuska, Joanna, E-mail: Joanna.Zembrzuska@put.poznan.pl; Budnik, Irena, E-mail: Irena.Budnik@gmail.com; Lukaszewski, Zenon, E-mail: zenon.lukaszewski@put.poznan.pl

    2016-07-01

    single unit. - Highlights: • Two parallel biodegradation pathways of alcohol ethoxylates have been discovered. • Apart from central fission, oxyethylene chain shortening has been evidenced. • Both a single Enterobacter strain and raw river water cause the same two pathways. • Ω-carboxylated alcohol ethoxylates are intermediate metabolites for chain shortening. • Homogeneous alcohol ethoxylate C{sub 12}E{sub 9} was the model used in this study.

  9. Topotactic conversion route to mesoporous quasi-single-crystalline Co{sub 3}O{sub 4} nanobelts with optimizable electrochemical performance

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Li [MOE Key Laboratory of Bioinorganic and Synthetic Chemistry State Key Laboratory of Optoelectronic Materials and Technology School of Chemistry and Chemical Engineering School of Physics and Engineering Sun Yat-Sen University Guangzhou, 510275 (China); School of Chemistry and Chemical Engineering, Hunan University of Science and Technology Xiangtan, 411201 (China); Zou, Hongli; Fu, Junxiang; Yang, Xianfeng; Wang, Yi; Fu, Xionghui; Liang, Chaolun; Wu, Mingmei; Shen, Pei Kang [MOE Key Laboratory of Bioinorganic and Synthetic Chemistry State Key Laboratory of Optoelectronic Materials and Technology School of Chemistry and Chemical Engineering School of Physics and Engineering Sun Yat-Sen University Guangzhou, 510275 (China); Guo, Hongliang; Gao, Qiuming [State Key Laboratory of High Performance Ceramics and Superfine Microstructures Shanghai Institute of Ceramics, Graduate School, Chinese Academy of Sciences 1295 Dingxi Rd., Shanghai 200050 (China)

    2010-02-22

    The growth of mesoporous quasi-single-crystalline Co{sub 3}O{sub 4} nanobelts by topotactic chemical transformation from {alpha}-Co(OH){sub 2} nanobelts is realized. During the topotactic transformation process, the primary {alpha}-Co(OH){sub 2} nanobelt frameworks can be preserved. The phases, crystal structures, morphologies, and growth behavior of both the precursory and resultant products are characterized by powder X-ray diffraction (XRD), electron microscopy - scanning electron (SEM) and transmission electron (TEM) microscopy, and selected area electron diffraction (SAED). Detailed investigation of the formation mechanism of the porous Co{sub 3}O{sub 4} nanobelts indicates topotactic nucleation and oriented growth of textured spinel Co{sub 3}O{sub 4} nanowalls (nanoparticles) inside the nanobelts. Co{sub 3}O{sub 4} nanocrystals prefer [0001] epitaxial growth direction of hexagonal {alpha}-Co(OH){sub 2} nanobelts due to the structural matching of [0001] {alpha}-Co(OH){sub 2}//[111] Co{sub 3}O{sub 4}. The surface-areas and pore sizes of the spinel Co{sub 3}O{sub 4} products can be tuned through heat treatment of {alpha}-Co(OH){sub 2} precursors at different temperatures. The galvanostatic cycling measurement of the Co{sub 3}O{sub 4} products indicates that their charge-discharge performance can be optimized. In the voltage range of 0.0-3.0 V versus Li{sup +}/Li at 40 mA g{sup -1}, reversible capacities of a sample consisting of mesoporous quasi-single-crystalline Co{sub 3}O{sub 4} nanobelts can reach up to 1400 mA h g{sup -1}, much larger than the theoretical capacity of bulk Co{sub 3}O{sub 4} (892 mA h g{sup -1}). (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  10. 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)

  11. 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)

  12. On the BER and capacity analysis of MIMO MRC systems with channel estimation error

    KAUST Repository

    Yang, Liang

    2011-10-01

    In this paper, we investigate the effect of channel estimation error on the capacity and bit-error rate (BER) of a multiple-input multiple-output (MIMO) transmit maximal ratio transmission (MRT) and receive maximal ratio combining (MRC) systems over uncorrelated Rayleigh fading channels. We first derive the ergodic (average) capacity expressions for such systems when power adaptation is applied at the transmitter. The exact capacity expression for the uniform power allocation case is also presented. Furthermore, to investigate the diversity order of MIMO MRT-MRC scheme, we derive the BER performance under a uniform power allocation policy. We also present an asymptotic BER performance analysis for the MIMO MRT-MRC system with multiuser diversity. The numerical results are given to illustrate the sensitivity of the main performance to the channel estimation error and the tightness of the approximate cutoff value. © 2011 IEEE.

  13. Allele specific LAMP- gold nanoparticle for characterization of single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Fábio Ferreira Carlos

    2017-12-01

    Full Text Available Due to their relevance as disease biomarkers and for diagnostics, screening of single nucleotide polymorphism (SNPs requires simple and straightforward strategies capable to provide results in medium throughput settings. Suitable approaches relying on isothermal amplification techniques have been evolving to substitute the cumbersome and highly specialized PCR amplification detection schemes. Nonetheless, identification of an individual’s genotype still requires sophisticated equipment and laborious methods.Here, we present a low-cost and reliable approach based on the allele specific loop-mediated isothermal amplification (AS-LAMP coupled to ssDNA functionalized gold nanoparticle (Au-nanoprobe colorimetric sequence discrimination. The Au-nanoprobe integration allows for the colorimetric detection of AS-LAMP amplification product that can be easily interpreted in less than 15 min. We targeted a clinical relevant SNP responsible for lactose intolerance (-13910C/T dbSNP rs#: 4988235 to demonstrate its proof of concept and full potential of this novel approach. Keywords: SNP, Isothermal amplification, Gold nanoparticles, Gold nanoprobes, Lactose intolerance

  14. Targeted detection of in vivo endogenous DNA base damage reveals preferential base excision repair in the transcribed strand.

    Science.gov (United States)

    Reis, António M C; Mills, Wilbur K; Ramachandran, Ilangovan; Friedberg, Errol C; Thompson, David; Queimado, Lurdes

    2012-01-01

    Endogenous DNA damage is removed mainly via base excision repair (BER), however, whether there is preferential strand repair of endogenous DNA damage is still under intense debate. We developed a highly sensitive primer-anchored DNA damage detection assay (PADDA) to map and quantify in vivo endogenous DNA damage. Using PADDA, we documented significantly higher levels of endogenous damage in Saccharomyces cerevisiae cells in stationary phase than in exponential phase. We also documented that yeast BER-defective cells have significantly higher levels of endogenous DNA damage than isogenic wild-type cells at any phase of growth. PADDA provided detailed fingerprint analysis at the single-nucleotide level, documenting for the first time that persistent endogenous nucleotide damage in CAN1 co-localizes with previously reported spontaneous CAN1 mutations. To quickly and reliably quantify endogenous strand-specific DNA damage in the constitutively expressed CAN1 gene, we used PADDA on a real-time PCR setting. We demonstrate that wild-type cells repair endogenous damage preferentially on the CAN1 transcribed strand. In contrast, yeast BER-defective cells accumulate endogenous damage preferentially on the CAN1 transcribed strand. These data provide the first direct evidence for preferential strand repair of endogenous DNA damage and documents the major role of BER in this process.

  15. Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways

    DEFF Research Database (Denmark)

    Do, Duy Ngoc; Ostersen, Tage; Strathe, Anders Bjerring

    2013-01-01

    Genome wide association studies (GWAS) are being extensively used in revealing genetic architecture of complex traits. However, GWAS offer limited understanding of the biological role of significant single nucleotide polymorphisms (SNPs) affecting complex traits. Pathway analysis using GWAS results...... is an important step where we firstly detect genes located near GWAS-detected SNPs and subsequently we detect enrichment of these genes in various biological processes and pathways. The objective of this study was to apply these steps to identify relevant pathways involved in residual feed intake (RFI) in pigs....... Residual feed intake is a feed efficiency measure and is highly economically important in animal production. In our study, a total of 596 Yorkshire boars had phenotypic and genotypic records. After quality control, 37,915 SNPs were available for GWAS which was implemented in the DMU software package...

  16. Storage temperature affects fruit quality attributes of Ber ( Ziziphus ...

    African Journals Online (AJOL)

    Fruit utilization is affected by quality attributes and shelf life. The quality of Jujube or Ber (Ziziphus mauritiana Lamk.) fruits after harvest depends on storage conditions used. In this study, different storage temperatures and durations were evaluated to determine the appropriate storage conditions of fresh fruits of Z.

  17. Decreased expression level of BER genes in Alzheimer's disease patients is not derivative of their DNA methylation status.

    Science.gov (United States)

    Sliwinska, Agnieszka; Sitarek, Przemysław; Toma, Monika; Czarny, Piotr; Synowiec, Ewelina; Krupa, Renata; Wigner, Paulina; Bialek, Katarzyna; Kwiatkowski, Dominik; Korycinska, Anna; Majsterek, Ireneusz; Szemraj, Janusz; Galecki, Piotr; Sliwinski, Tomasz

    2017-10-03

    Neurodegeneration in Alzheimer's disease can be caused by accumulation of oxidative DNA damage resulting from altered expression of genes involved in the base excision repair system (BER). Promoter methylation can affect the profile of BER genes expression. Decreased expression of BER genes was observed in the brains of AD patients. The aim of our study was to compare the expression and methylation profiles of six genes coding for proteins involved in BER, namely: hOGG1, APE1, MUTYH, NEIL1, PARP1 and XRCC1, in the peripheral blood cells of AD patients and healthy volunteers. The study consisted of 100 persons diagnosed with Alzheimer's disease according to DSM-IV criteria, and 110 healthy volunteers. DNA and total RNA were isolated from venous blood cells. Promoter methylation profiles were obtained by High Resolution Melting (HRM) analysis of bisulfide converted DNA samples. Real-time PCR with TaqMan probes was employed for gene expression analysis. APE1, hOGG1, MUTYH, PARP1 and NEIL1 were significantly (pgenes. The methylation status of promoters is not associated with downregulation of BER genes. Our results show that downregulation of BER genes detected in peripheral blood samples could reflect the changes occurring in the brain of patients with AD, and may be a useful biomarker of this disease. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Single-gene testing combined with single nucleotide polymorphism microarray preimplantation genetic diagnosis for aneuploidy: a novel approach in optimizing pregnancy outcome.

    Science.gov (United States)

    Brezina, Paul R; Benner, Andrew; Rechitsky, Svetlana; Kuliev, Anver; Pomerantseva, Ekaterina; Pauling, Dana; Kearns, William G

    2011-04-01

    To describe a method of amplifying DNA from blastocyst trophectoderm cells (two or three cells) and simultaneously performing 23-chromosome single nucleotide polymorphism microarrays and single-gene preimplantation genetic diagnosis. Case report. IVF clinic and preimplantation genetic diagnostic centers. A 36-year-old woman, gravida 2, para 1011, and her husband who both were carriers of GM(1) gangliosidosis. The couple wished to proceed with microarray analysis for aneuploidy detection coupled with DNA sequencing for GM(1) gangliosidosis. An IVF cycle was performed. Ten blastocyst-stage embryos underwent trophectoderm biopsy. Twenty-three-chromosome microarray analysis for aneuploidy and specific DNA sequencing for GM(1) gangliosidosis mutations were performed. Viable pregnancy. After testing, elective single embryo transfer was performed followed by an intrauterine pregnancy with documented fetal cardiac activity by ultrasound. Twenty-three-chromosome microarray analysis for aneuploidy detection and single-gene evaluation via specific DNA sequencing and linkage analysis are used for preimplantation diagnosis for single-gene disorders and aneuploidy. Because of the minimal amount of genetic material obtained from the day 3 to 5 embryos (up to 6 pg), these modalities have been used in isolation of each other. The use of preimplantation genetic diagnosis for aneuploidy coupled with testing for single-gene disorders via trophectoderm biopsy is a novel approach to maximize pregnancy outcomes. Although further investigation is warranted, preimplantation genetic diagnosis for aneuploidy and single-gene testing seem destined to be used increasingly to optimize ultimate pregnancy success. Copyright © 2011 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  19. Tunable White-Light Emission in Single-Cation-Templated Three-Layered 2D Perovskites (CH <sub>3sub> CH <sub>2sub> NH <sub>3sub> ) <sub>4sub> Pb <sub>3sub> Br <sub>10–xsub> Cl <sub>x>

    Energy Technology Data Exchange (ETDEWEB)

    Mao, Lingling; Wu, Yilei; Stoumpos, Constantinos C.; Traore, Boubacar [Institut; Katan, Claudine [Institut; Even, Jacky [Fonctions; Wasielewski, Michael R.; Kanatzidis, Mercouri G.

    2017-08-16

    Two-dimensional (2D) hybrid halide perovskites come as a family (B)<sub>2sub>(A)>n-1sub>PbnX>3n+1sub> (B and A= cations; X= halide). These perovskites are promising semiconductors for solar cells and optoelectronic applications. Among the fascinating properties of these materials is white-light emission, which has been mostly observed in single-layered 2D lead bromide or chloride systems (n = 1), where the broad emission comes from the transient photoexcited states generated by self-trapped excitons (STEs) from structural distortion. Here we report a multilayered 2D perovskite (n = 3) exhibiting a tunable white-light emission. Ethylammonium (EA+) can stabilize the 2D perovskite structure in EA<sub>4sub>Pb>3sub>Br>10–xsub>Clx> (x = 0, 2, 4, 6, 8, 9.5, and 10) with EA+ being both the A and B cations in this system. Because of the larger size of EA, these materials show a high distortion level in their inorganic structures, with EA4Pb3Cl10 having a much larger distortion than that of EA<sub>4sub>Pb>3sub>Br>10sub>, which results in broadband white-light emission of EA<sub>4sub>Pb>3sub>Cl>10sub> in contrast to narrow blue emission of EA4Pb3Br10. The average lifetime of the series decreases gradually from the Cl end to the Br end, indicating that the larger distortion also prolongs the lifetime (more STE states). The band gap of EA<sub>4sub>Pb>3sub>Br>10–xsub>Clx> ranges from 3.45 eV (x = 10) to 2.75 eV (x = 0), following Vegard’s law. First-principles density functional theory calculations (DFT) show that both EA<sub>4sub>Pb>3sub>Cl>10sub> and EA<sub>4sub>Pb>3sub>Br>10sub> are direct band gap semiconductors. The color rendering index (CRI) of the series improves from 66 (EA<sub>4sub>Pb>3sub>Cl>10sub>) to 83 (EA<sub>4sub>Pb>3sub>Br>0.5sub>Cl>9.5sub>), displaying high tunability and versatility of the

  20. Influence of XRCC1 Genetic Polymorphisms on Ionizing Radiation-Induced DNA Damage and Repair

    Directory of Open Access Journals (Sweden)

    Silvia Sterpone

    2010-01-01

    Full Text Available It is well known that ionizing radiation (IR can damage DNA through a direct action, producing single- and double-strand breaks on DNA double helix, as well as an indirect effect by generating oxygen reactive species in the cells. Mammals have evolved several and distinct DNA repair pathways in order to maintain genomic stability and avoid tumour cell transformation. This review reports important data showing a huge interindividual variability on sensitivity to IR and in susceptibility to developing cancer; this variability is principally represented by genetic polymorphisms, that is, DNA repair gene polymorphisms. In particular we have focussed on single nucleotide polymorphisms (SNPs of XRCC1, a gene that encodes for a scaffold protein involved basically in Base Excision Repair (BER. In this paper we have reported and presented recent studies that show an influence of XRCC1 variants on DNA repair capacity and susceptibility to breast cancer.

  1. Influence of XRCC1 Genetic Polymorphisms on Ionizing Radiation-Induced DNA Damage and Repair.

    Science.gov (United States)

    Sterpone, Silvia; Cozzi, Renata

    2010-07-25

    It is well known that ionizing radiation (IR) can damage DNA through a direct action, producing single- and double-strand breaks on DNA double helix, as well as an indirect effect by generating oxygen reactive species in the cells. Mammals have evolved several and distinct DNA repair pathways in order to maintain genomic stability and avoid tumour cell transformation. This review reports important data showing a huge interindividual variability on sensitivity to IR and in susceptibility to developing cancer; this variability is principally represented by genetic polymorphisms, that is, DNA repair gene polymorphisms. In particular we have focussed on single nucleotide polymorphisms (SNPs) of XRCC1, a gene that encodes for a scaffold protein involved basically in Base Excision Repair (BER). In this paper we have reported and presented recent studies that show an influence of XRCC1 variants on DNA repair capacity and susceptibility to breast cancer.

  2. Modeling Li-ion conductivity in LiLa(PO{sub 3}){sub 4} powder

    Energy Technology Data Exchange (ETDEWEB)

    Mounir, Ferhi, E-mail: ferhi.mounir@gmail.com [Laboratoire de Physicochimie des Materiaux Mineraux et leurs Applications, Centre National des Recherches en Sciences des Materiaux, BP No. 73, 8027 Soliman (Tunisia); Karima, Horchani-Naifer [Laboratoire de Physicochimie des Materiaux Mineraux et leurs Applications, Centre National des Recherches en Sciences des Materiaux, BP No. 73, 8027 Soliman (Tunisia); Khaled, Ben Saad [Laboratoire de Photovoltaieque, Centre des Recherches et des Technologies de l' Energie, Technopole Borj Cedria, BP No. 95, 2050 Hammam Lif (Tunisia); Mokhtar, Ferid [Laboratoire de Physicochimie des Materiaux Mineraux et leurs Applications, Centre National des Recherches en Sciences des Materiaux, BP No. 73, 8027 Soliman (Tunisia)

    2012-07-01

    Polycrystalline powder and single-crystal of LiLa(PO{sub 3}){sub 4} are synthesized by solid state reaction and flux technique, respectively. A morphological description of the obtained product was made based on scanning electron microscopy micrographs. The obtained powder was characterized by X-ray powder diffraction, FTIR and Raman spectroscopies. Ionic conductivity of the LiLa(PO{sub 3}){sub 4} powder was measured and evaluated over a temperature range from 553 to 913 K. Single crystals of LiLa(PO{sub 3}){sub 4} are characterized by single-crystal X-ray diffraction. The LiLa(PO{sub 3}){sub 4} structure was found to be isotypic with LiNd(PO{sub 3}){sub 4}. It crystallizes in the monoclinic system with space group C2/c and cell parameters: a=16.635(6) A, b=7.130(3) A, c=9.913(3) A, {beta}=126.37(4) Degree-Sign , V=946.72(6) A{sup 3} and Z=4. The LiLa(PO{sub 3}){sub 4} structure was described as an alternation between spiraling chains (PO{sub 3}){sub n} and (La{sup 3+}, Li{sup +}) cations along the b direction. The small Li{sup +} ions, coordinated to four oxygen atoms, were located in the large connected cavities created between the LaO{sub 8} polyhedra and the polyphosphate chains. The jumping of Li{sup +} through tunnels of the crystalline network was investigated using complex impedance spectroscopy. The close value of the activation energies calculated through the analysis of conductivity data and loss spectra indicate that the transport in the investigated system is through hopping mechanism. The correlation between ionic conductivity of LiLa(PO{sub 3}){sub 4} and its crystallographic structure was investigated and the most probably transport pathway model was determined.

  3. Czochralski growth and characterization of {beta}-Ga{sub 2}O{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Galazka, Z.; Uecker, R.; Irmscher, K.; Albrecht, M.; Klimm, D.; Pietsch, M.; Bruetzam, M.; Bertram, R.; Ganschow, S.; Fornari, R. [Leibniz Institute for Crystal Growth, Max-Born-Str. 2, 12489 Berlin (Germany)

    2010-12-15

    Transparent semiconducting {beta}-Ga{sub 2}O{sub 3} single crystals were grown by the Czochralski method from an iridium crucible under a dynamic protective atmosphere to control partial pressures of volatile species of Ga{sub 2}O{sub 3}. Thermodynamic calculations on different atmospheres containing CO{sub 2}, Ar and O{sub 2} reveal that CO{sub 2} growth atmosphere combined with overpressure significantly decreases evaporation of volatile Ga{sub 2}O{sub 3} species without any harm to iridium crucible. It has been found that CO{sub 2}, besides providing high oxygen concentration at high temperatures, is also acting as a minor reducing agent for Ga{sub 2}O{sub 3}. Different coloration of obtained crystals as well as optical and electrical properties are directly correlated with growth conditions (atmosphere, pressure and temperature gradients), but not with residual impurities. Typical electrical properties of the n-type {beta}-Ga{sub 2}O{sub 3} crystals at room temperature are: {rho} = 0.1 - 0.3 {omega}cm, {mu}{sub n,Hall} = 110 - 150 cm{sup 2}V{sup -1}s{sup -1}, n{sub Hall} = 2 - 6 x 10{sup 17} cm{sup -3} and E{sub Ionisation} = 30 - 40 meV. A decrease of transmission in the IR-region is directly correlated with the free carrier concentration and can be effectively modulated by the dynamic growth atmosphere. Electron paramagnetic resonance (EPR) spectra exhibit an isotropic shallow donor level and anisotropic defect level. According to differential thermal analysis (DTA) measurements, there is substantially no mass change of {beta}-Ga{sub 2}O{sub 3} crystals below 1200 C (i.e. no decomposition) under oxidizing or neutral atmosphere, while the mass gradually decreases with temperature above 1200 C. High resolution transmission electron microscopy (HRTEM) images at atomic resolution show the presence of vacancies, which can be attributed to Ga or O sites, and interstitials, which can likely be attributed to Ga atoms. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGa

  4. Scintillation and optical properties of Ce{sup 3+}-doped CaGdAl{sub 3}O{sub 7} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Masaki, E-mail: masaki.mori.mz4@ms.naist.jp [Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192 (Japan); Nakauchi, Daisuke; Okada, Go [Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192 (Japan); Fujimoto, Yutaka [Department of Applied Chemistry, Graduate School of Engineering, Tohoku University, 6-6-07 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579 (Japan); Kawaguchi, Noriaki [Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192 (Japan); Koshimizu, Masanori [Department of Applied Chemistry, Graduate School of Engineering, Tohoku University, 6-6-07 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579 (Japan); Yanagida, Takayuki [Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0192 (Japan)

    2017-06-15

    The single crystals of 0, 0.6, 1, 1.6 and 2 mol% Ce doped CaGdAl{sub 3}O{sub 7} (Ce:CGAM) were grown by the Floating Zone method, and investigated on photoluminescence (PL) and scintillation properties. In the PL spectra, a broad emission appeared over 380–500 nm under 280 and 360 nm excitations with the quantum yield of 33.8–38.8%. Under a vacuum ultraviolet excitation (90 nm) using a synchrotron source, non-doped CGAM single crystal showed broad emissions over 250–650 nm. The PL decay time profiles followed a monotonic exponential decay with a decay time constant of around 33 ns. The scintillation spectra were similar to those of PL. All of the samples exhibited a clear photoabsorption peak and Compton edge in the pulse height spectra measured under {sup 137}Cs γ-ray irradiation, and the absolute scintillation light yield (LY) was highest for the 2% Ce-doped sample with the value of 3300±300 ph/MeV. The scintillation decay profiles were approximated by a third order exponential decay function, and the extracted decay time of Ce{sup 3+} emission component was around 36–44 ns. Among all the samples, 2%Ce:CGAM single crystal sample showed the best afterglow level as a scintillator under X-ray irradiation. - Highlights: •Ce{sup 3+}-doped CaGdAl{sub 3}O{sub 7} single crystals were synthesized by the FZ method. •Optical and scintillation properties of Ce{sup 3+}-doped CaGdAl{sub 3}O{sub 7} were investigated. •Photoabsorption peak in a pulse height spectrum was clearly observed under γ-rays.

  5. Electromagnetic and microwave absorption properties of single-walled carbon nanotubes and CoFe{sub 2}O{sub 4} nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Li, Guo; Sheng, Leimei, E-mail: slmss@shu.edu.cn; Yu, Liming; An, Kang; Ren, Wei; Zhao, Xinluo, E-mail: xlzhao@shu.edu.cn

    2015-03-15

    Highlights: • LPA-SWCNTs have been abundantly fabricated by a facile, time-saving, economical and non-hazardous method using DC arc discharge technique in low-pressure air. • The electromagnetic and microwave absorption properties of LPA-SWCNTs, CoFe{sub 2}O{sub 4} nanocrystals and LPA-SWCNT/CoFe{sub 2}O{sub 4} nanocomposites were investigated and the LPA-SWCNT/CoFe{sub 2}O{sub 4} nanocomposites exhibited excellent microwave absorption properties. • The Debye theory and impedance matching were used to analyze the electromagnetic parameters and microwave absorption properties. - Abstract: Single-walled carbon nanotubes were facilely and abundantly synthesized by low-pressure air arc discharge method (LPA-SWCNTs), and CoFe{sub 2}O{sub 4} nanocrystals were synthesized by a nitrate citric acid sol–gel auto-ignition method. The electromagnetic and microwave absorption properties of LPA-SWCNTs, CoFe{sub 2}O{sub 4} nanocrystals and their nanocomposites were investigated. The LPA-SWCNT/CoFe{sub 2}O{sub 4} nanocomposites showed excellent microwave absorption properties. The minimum efficient reflection loss is −30.7 dB at 12.9 GHz for 10 wt% of LPA-SWCNTs in the nanocomposites, and an effective absorption bandwidth with a reflection loss below −10 dB is 7.2 GHz. The Debye equation and impedance matching were introduced to explain the microwave absorption properties. Compared with the single-component materials, the LPA-SWCNT/CoFe{sub 2}O{sub 4} nanocomposites are an excellent candidate for microwave absorbers.

  6. Synthesis of BiFeO{sub 3} thin films on single-terminated Nb : SrTiO{sub 3} (111) substrates by intermittent microwave assisted hydrothermal method

    Energy Technology Data Exchange (ETDEWEB)

    Velasco-Davalos, Ivan; Ambriz-Vargas, Fabian; Kolhatkar, Gitanjali; Thomas, Reji, E-mail: ruediger@emt.inrs.ca, E-mail: reji.thomas@emt.inrs.ca; Ruediger, Andreas, E-mail: ruediger@emt.inrs.ca, E-mail: reji.thomas@emt.inrs.ca [Centre Énergie, Matériaux et Télécommunications, INRS, 1650 Lionel-Boulet, Varennes, Québec, J3X1S2 (Canada)

    2016-06-15

    We report on a simple and fast procedure to create arrays of atomically flat terraces on single crystal SrTiO{sub 3} (111) substrates and the deposition of ferroelectric BiFeO{sub 3} thin films on such single-terminated surfaces. A microwave-assisted hydrothermal method in deionized water and ammonia solution selectively removes either (SrO{sub 3}){sup 4−} or Ti{sup 4+} layers to ensure the same chemical termination on all terraces. Measured step heights of 0.225 nm (d{sub 111}) and uniform contrast in the phase image of the terraces confirm the single termination in pure and Nb doped SrTiO{sub 3} single crystal substrates. Multiferroic BiFeO{sub 3} thin films were then deposited by the same microwave assisted hydrothermal process on Nb : SrTiO{sub 3} (111) substrates. Bi(NO{sub 3}){sub 3} and Fe(NO{sub 3}){sub 3} along with KOH served as the precursors solution. Ferroelectric behavior of the BiFeO{sub 3} films on Nb : SrTiO{sub 3} (100) substrates was verified by piezoresponse force microscopy.

  7. A single nucleotide polymorphism within the acetyl-coenzyme A carboxylase beta gene is associated with proteinuria in patients with type 2 diabetes

    DEFF Research Database (Denmark)

    Maeda, Shiro; Kobayashi, Masa-aki; Araki, Shin-ichi

    2010-01-01

    It has been suggested that genetic susceptibility plays an important role in the pathogenesis of diabetic nephropathy. A large-scale genotyping analysis of gene-based single nucleotide polymorphisms (SNPs) in Japanese patients with type 2 diabetes identified the gene encoding acetyl-coenzyme A ca...

  8. Inhomogeneous electronic structures in heavily Pb-doped Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub y} single crystals probed by low temperature STM/STS

    Energy Technology Data Exchange (ETDEWEB)

    Kinoda, Go; Nakao, Shoichiro; Motohashi, Teruki; Nakayama, Yuri; Shimizu, Keisuke; Shimoyama, Junichi; Kishio, Koji; Hanaguri, Tetsuo; Kitazawa, Koichi; Hasegawa, Tetsuya

    2003-05-15

    We have performed cryogenic scanning tunneling microscopy/spectroscopy (STM/STS) of heavily Pb-doped Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub y} single crystals to investigate local electronic structures in the overdoped regime. The obtained STM/STS results at 4.3 K clearly showed local inhomogeneity of gap structure {delta} ({delta}=20-60 meV) in a scale of several nm, suggesting the coexistence of superconducting and pseudogap-like regions, even in the overdoped regime.

  9. Makeup of the genetic correlation between milk production traits using genome-wide single nucleotide polymorphism information.

    Science.gov (United States)

    van Binsbergen, R; Veerkamp, R F; Calus, M P L

    2012-04-01

    The correlated responses between traits may differ depending on the makeup of genetic covariances, and may differ from the predictions of polygenic covariances. Therefore, the objective of the present study was to investigate the makeup of the genetic covariances between the well-studied traits: milk yield, fat yield, protein yield, and their percentages in more detail. Phenotypic records of 1,737 heifers of research farms in 4 different countries were used after homogenizing and adjusting for management effects. All cows had a genotype for 37,590 single nucleotide polymorphisms (SNP). A bayesian stochastic search variable selection model was used to estimate the SNP effects for each trait. About 0.5 to 1.0% of the SNP had a significant effect on 1 or more traits; however, the SNP without a significant effect explained most of the genetic variances and covariances of the traits. Single nucleotide polymorphism correlations differed from the polygenic correlations, but only 10 regions were found with an effect on multiple traits; in 1 of these regions the DGAT1 gene was previously reported with an effect on multiple traits. This region explained up to 41% of the variances of 4 traits and explained a major part of the correlation between fat yield and fat percentage and contributes to asymmetry in correlated response between fat yield and fat percentage. Overall, for the traits in this study, the infinitesimal model is expected to be sufficient for the estimation of the variances and covariances. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  10. Association of STAT4 gene single nucleotide polymorphisms with Iranian juvenile-onset systemic lupus erythematosus patients.

    Science.gov (United States)

    Salmaninejad, Arash; Mahmoudi, Mahdi; Aslani, Saeed; Poursani, Shiva; Ziaee, Vahid; Rezaei, Nima

    2017-01-01

    Salmaninejad A, Mahmoudi M, Aslani S, Poursani S, Ziaee V, Rezaei N. Association of STAT4 gene single nucleotide polymorphisms with Iranian juvenile-onset systemic lupus erythematosus patients. Turk J Pediatr 2017; 59: 144-149. Juvenile-onset systemic lupus erythematosus (JSLE) is a complex autoimmune disease, characterized by multi-organ involvement. Single nucleotide polymorphisms (SNPs) of signal transducer and activator of transcription 4 (STAT4) gene have been reported to have relationship with the risk of several autoimmune diseases. Studies have provided evidence that STAT4 may participate in the pathogenesis of JSLE. Therefore, we aimed to evaluate the association of STAT4 SNPs with JSLE in Iranian population. In this case-control study, two SNPs of STAT4 gene, including rs7574865 and rs7601754 were genotyped in 50 Iranian JSLE patients and 281 matched healthy individuals using real-time PCR allelic discrimination approach. Our experiments demonstrated that G and T alleles of rs7574865 SNP had similar distribution between patients and controls (P = 0.16). Additionally, differences in frequency of GG, GT, and TT genotypes (P = 0.14, 0.29, and 0.54, respectively) were not significant. Likewise, A and G alleles, as well as genotypes of rs7601754 SNP did not show significant differences between JSLE patients and healthy individuals. Lack of association of rs7574865 and rs7601754 SNPs in STAT4 gene with susceptibility to JSLE in Iranian population, despite their association with the risk of adult SLE in the same population, implicates on difference of genetic background of JSLE and SLE.

  11. CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

    Science.gov (United States)

    Wong, Wing Chung; Kim, Dewey; Carter, Hannah; Diekhans, Mark; Ryan, Michael C; Karchin, Rachel

    2011-08-01

    Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python 5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM.

  12. Single Nucleotide Polymorphism Identification, Characterization, and Linkage Mapping in Quinoa

    Directory of Open Access Journals (Sweden)

    P. J. Maughan

    2012-11-01

    Full Text Available Quinoa ( Willd. is an important seed crop throughout the Andean region of South America. It is important as a regional food security crop for millions of impoverished rural inhabitants of the Andean Altiplano (high plains. Efforts to improve the crop have led to an increased focus on genetic research. We report the identification of 14,178 putative single nucleotide polymorphisms (SNPs using a genomic reduction protocol as well as the development of 511 functional SNP assays. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 113 quinoa accessions showed that the minor allele frequency (MAF of the SNPs ranged from 0.02 to 0.50, with an average MAF of 0.28. Structure analysis of the quinoa diversity panel uncovered the two major subgroups corresponding to the Andean and coastal quinoa ecotypes. Linkage mapping of the SNPs in two recombinant inbred line populations produced an integrated linkage map consisting of 29 linkage groups with 20 large linkage groups, spanning 1404 cM with a marker density of 3.1 cM per SNP marker. The SNPs identified here represent important genomic tools needed in emerging plant breeding programs for advanced genetic analysis of agronomic traits in quinoa.

  13. Risk of the research reactor BER II in Berlin; Risiken des Berliner Experimentierreaktors BER II

    Energy Technology Data Exchange (ETDEWEB)

    Paulitz, Henrik; Hoevener, Barbara; Rosen, Alex

    2015-04-20

    The research reactor BER II is sited at the periphery of Berlin in the neighborhood of residential areas. The operational license is limited until December 31, 2019. The reactor is funded by the Federal Government (90%) and the city of Berlin (10%). The stress test has shown that the reactor is not secured against an aircraft crash (airliner or fast flying military jet), meltdown with remarkable radiological consequences to the public would be the consequence. Further hazards result from the radioactive waste transport, explosions and fires. The emergency measures cannot be considered to be sufficient. The city of Berlin would not be able to fulfill the required measures in case of a radiation accident.

  14. Synthesis, structure and optical properties of single-crystalline In{sub 2}O{sub 3} nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Hadia, N.M.A., E-mail: nomery_abass@yahoo.com [Physics Department, Faculty of Science, Sohag University, 82524 Sohag (Egypt); Mohamed, H.A. [Physics Department, Faculty of Science, Sohag University, 82524 Sohag (Egypt); King Saud University, Teachers College, Science Department (Physics), 11148 Riyadh (Saudi Arabia)

    2013-01-15

    Highlights: Black-Right-Pointing-Pointer Metal and metal oxide one dimensional (1D) nanostructured materials are of crucial importance. Black-Right-Pointing-Pointer The paper deals with the synthesis of In{sub 2}O{sub 3} nanowires without the use of catalysts. Black-Right-Pointing-Pointer The optical constants and Photoluminescence (PL) of In{sub 2}O{sub 3} nanowires were evaluated. - Abstract: Indium oxide In{sub 2}O{sub 3} nanowires have been recently synthesized revealing interesting properties and used in various applications. In order to reduce as much as possible the influence of undesired dopants and/or impurities on the observed properties, In{sub 2}O{sub 3} nanowires have been grown without the use of catalysts, directly from metallic indium by a vapor transport technique and a controlled oxidation with oxygen-argon mixtures. Depending on the growth conditions (temperature, vapor pressure, oxygen concentration, etc.) different results have been achieved and it has been observed that a 'proper' In condensation on the substrates may enhance the nanowires growth. Detailed structural analysis showed that the In{sub 2}O{sub 3} nanostructures are single crystalline with a cubic crystal structure. The grown In{sub 2}O{sub 3} nanowires were optically characterized in order to evaluate the absorption coefficient, optical band gap, refractive index and extinction coefficient. Room temperature Photoluminescence (PL) spectrum showed broad and intense blue emission at 375 nm.

  15. Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm.

    Science.gov (United States)

    Zhou, Lin; Matsumoto, Tracie; Tan, Hua-Wei; Meinhardt, Lyndel W; Mischke, Sue; Wang, Boyi; Zhang, Dapeng

    2015-01-01

    Pineapple (Ananas comosus [L.] Merr.) is the third most important tropical fruit in the world after banana and mango. As a crop with vegetative propagation, genetic redundancy is a major challenge for efficient genebank management and in breeding. Using expressed sequence tag and nucleotide sequences from public databases, we developed 213 single nucleotide polymorphism (SNP) markers and validated 96 SNPs by genotyping the United States Department of Agriculture - Agricultural Research Service pineapple germplasm collection, maintained in Hilo, Hawaii. The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection. Twenty-four groups of duplicates were detected, encompassing 130 of the total 170 A cosmos accessions. The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple. Multivariate clustering and a model-based population stratification suggest that the modern pineapple cultivars are comprised of progenies that are derived from different wild Ananas botanical varieties. Parentage analysis further revealed that both A. comosus var. bracteatus and A. comosus var. ananassoides are likely progenitors of pineapple cultivars. However, the traditional classification of cultivated pineapple into horticultural groups (e.g. 'Cayenne', 'Spanish', 'Queen') was not well supported by the present study. These SNP markers provide robust and universally comparable DNA fingerprints; thus, they can serve as an efficient genotyping tool to assist pineapple germplasm management, propagation of planting material, and pineapple cultivar protection. The high rate of genetic redundancy detected in this pineapple collection suggests the potential impact of applying this technology on other clonally propagated perennial crops.

  16. Assembly of inflammation-related genes for pathway-focused genetic analysis.

    Directory of Open Access Journals (Sweden)

    Matthew J Loza

    2007-10-01

    Full Text Available Recent identifications of associations between novel variants in inflammation-related genes and several common diseases emphasize the need for systematic evaluations of these genes in disease susceptibility. Considering that many genes are involved in the complex inflammation responses and many genetic variants in these genes have the potential to alter the functions and expression of these genes, we assembled a list of key inflammation-related genes to facilitate the identification of genetic associations of diseases with an inflammation-related etiology. We first reviewed various phases of inflammation responses, including the development of immune cells, sensing of danger, influx of cells to sites of insult, activation and functional responses of immune and non-immune cells, and resolution of the immune response. Assisted by the Ingenuity Pathway Analysis, we then identified 17 functional sub-pathways that are involved in one or multiple phases. This organization would greatly increase the chance of detecting gene-gene interactions by hierarchical clustering of genes with their functional closeness in a pathway. Finally, as an example application, we have developed tagging single nucleotide polymorphism (tSNP arrays for populations of European and African descent to capture all the common variants of these key inflammation-related genes. Assays of these tSNPs have been designed and assembled into two Affymetrix ParAllele customized chips, one each for European (12,011 SNPs and African (21,542 SNPs populations. These tSNPs have greater coverage for these inflammation-related genes compared to the existing genome-wide arrays, particularly in the African population. These tSNP arrays can facilitate systematic evaluation of inflammation pathways in disease susceptibility. For additional applications, other genotyping platforms could also be employed. For existing genome-wide association data, this list of key inflammation-related genes and

  17. Inhibition of nucleotide excision repair by fludarabine in normal lymphocytes in vitro, measured by the alkaline single cell gel electrophoresis (comet) assay

    Energy Technology Data Exchange (ETDEWEB)

    Yamauchi, Takahiro; Kawai, Yasukazu; Ueda, Takanori [Fukui Medical Univ., Matsuoka (Japan)

    2002-05-01

    Alkylating agents or platinum analogues initiate several excision repair mechanisms, which involve incision of the DNA strand, excision of the damaged nucleotide, gap filling by DNA resynthesis, and rejoining by ligation. The previous study described that nucleotide excision repair permitted incorporation of fludarabine nucleoside (F-area-A) into the repair patch, thereby inhibiting the DNA resynthesis. In the present study, to clarify the repair kinetics in view of the inhibition by F-ara-A, normal lymphocytes were stimulated to undergo nucleotide excision repair by ultraviolet C (UV) irradiation in the presence or absence of F-ara-A. The repair kinetics were determined as DNA single strand breaks resulting from the incision and the rejoining using the alkaline single cell gel electrophoresis (comet) assay. DNA resynthesis was evaluated in terms of the uptake of tritiated thymidine into DNA. The lymphocytes initiated the incision step maximally at 1 h, and completed the rejoining process within 4 h after UV exposure. UV also initiated thymidine uptake, which increased time-dependently and reached a plateau at 4 h. A 2-h pre-incubation with F-ara-A inhibited the repair in a concentration-dependent manner, with the maximal inhibition by 5 {mu}M. This inhibitory effect was demonstrated by the reduction of the thymidine uptake and by the inhibition of the rejoining. A DNA polymerase inhibitor, aphidicolin, and a ribonucleotide reductase inhibitor, hydroxyurea, were not so inhibitory to the repair process as F-ara-A at equimolar concentrations. The present findings suggest that inhibition of nucleotide excision repair may represent a novel therapeutic strategy against cancer, especially in the context of resistant cells with an increased repair capacity. (author)

  18. FRAS1-related extracellular matrix 3 (FREM3) single-nucleotide polymorphism effects on gene expression, amygdala reactivity and perceptual processing speed: An accelerated aging pathway of depression risk

    Science.gov (United States)

    Nikolova, Yuliya S.; Iruku, Swetha P.; Lin, Chien-Wei; Conley, Emily Drabant; Puralewski, Rachel; French, Beverly; Hariri, Ahmad R.; Sibille, Etienne

    2015-01-01

    The A allele of the FRAS1-related extracellular matrix protein 3 (FREM3) rs7676614 single nucleotide polymorphism (SNP) was linked to major depressive disorder (MDD) in an early genome-wide association study (GWAS), and to symptoms of psychomotor retardation in a follow-up investigation. In line with significant overlap between age- and depression-related molecular pathways, parallel work has shown that FREM3 expression in postmortem human brain decreases with age. Here, we probe the effect of rs7676614 on amygdala reactivity and perceptual processing speed, both of which are altered in depression and aging. Amygdala reactivity was assessed using a face-matching BOLD fMRI paradigm in 365 Caucasian participants in the Duke Neurogenetics Study (DNS) (192 women, mean age 19.7 ± 1.2). Perceptual processing speed was indexed by reaction times in the same task and the Trail Making Test (TMT). The effect of rs7676614 on FREM3 mRNA brain expression levels was probed in a postmortem cohort of 169 Caucasian individuals (44 women, mean age 50.8 ± 14.9). The A allele of rs7676614 was associated with blunted amygdala reactivity to faces, slower reaction times in the face-matching condition (p < 0.04), as well as marginally slower performance on TMT Part B (p = 0.056). In the postmortem cohort, the T allele of rs6537170 (proxy for the rs7676614 A allele), was associated with trend-level reductions in gene expression in Brodmann areas 11 and 47 (p = 0.066), reminiscent of patterns characteristic of older age. The low-expressing allele of another FREM3 SNP (rs1391187) was similarly associated with reduced amygdala reactivity and slower TMT Part B speed, in addition to reduced BA47 activity and extraversion (p < 0.05). Together, these results suggest common genetic variation associated with reduced FREM3 expression may confer risk for a subtype of depression characterized by reduced reactivity to environmental stimuli and slower perceptual processing speed, possibly suggestive of

  19. Effect of Pointing Error on the BER Performance of an Optical CDMA FSO Link with SIK Receiver

    Science.gov (United States)

    Nazrul Islam, A. K. M.; Majumder, S. P.

    2017-12-01

    An analytical approach is presented for an optical code division multiple access (OCDMA) system over free space optical (FSO) channel considering the effect of pointing error between the transmitter and the receiver. Analysis is carried out with an optical sequence inverse keying (SIK) correlator receiver with intensity modulation and direct detection (IM/DD) to find the bit error rate (BER) with pointing error. The results are evaluated numerically in terms of signal-to-noise plus multi-access interference (MAI) ratio, BER and power penalty due to pointing error. It is noticed that the OCDMA FSO system is highly affected by pointing error with significant power penalty at a BER of 10-6 and 10-9. For example, penalty at BER 10-9 is found to be 9 dB corresponding to normalized pointing error of 1.4 for 16 users with processing gain of 256 and is reduced to 6.9 dB when the processing gain is increased to 1,024.

  20. Solution structure, copper binding and backbone dynamics of recombinant Ber e 1-the major allergen from Brazil nut.

    Directory of Open Access Journals (Sweden)

    Louise Rundqvist

    Full Text Available BACKGROUND: The 2S albumin Ber e 1 is the major allergen in Brazil nuts. Previous findings indicated that the protein alone does not cause an allergenic response in mice, but the addition of components from a Brazil nut lipid fraction were required. Structural details of Ber e 1 may contribute to the understanding of the allergenic properties of the protein and its potential interaction partners. METHODOLOGY/PRINCIPAL FINDINGS: The solution structure of recombinant Ber e 1 was solved using NMR spectroscopy and measurements of the protein back bone dynamics at a residue-specific level were extracted using (15N-spin relaxation. A hydrophobic cavity was identified in the structure of Ber e 1. Using the paramagnetic relaxation enhancement property of Cu(2+ in conjunction with NMR, it was shown that Ber e 1 is able to specifically interact with the divalent copper ion and the binding site was modeled into the structure. The IgE binding region as well as the copper binding site show increased dynamics on both fast ps-ns timescale as well as slower µs-ms timescale. CONCLUSIONS/SIGNIFICANCE: The overall fold of Ber e 1 is similar to other 2S albumins, but the hydrophobic cavity resembles that of a homologous non-specific lipid transfer protein. Ber e 1 is the first 2S albumin shown to interact with Cu(2+ ions. This Cu(2+ binding has minimal effect on the electrostatic potential on the surface of the protein, but the charge distribution within the hydrophobic cavity is significantly altered. As the hydrophobic cavity is likely to be involved in a putative lipid interaction the Cu(2+ can in turn affect the interaction that is essential to provoke an allergenic response.

  1. Polymorphisms in base excision repair genes as colorectal cancer risk factors and modifiers of the effect of diets high in red meat.

    Science.gov (United States)

    Brevik, Asgeir; Joshi, Amit D; Corral, Román; Onland-Moret, N Charlotte; Siegmund, Kimberly D; Le Marchand, Loïc; Baron, John A; Martinez, Maria Elena; Haile, Robert W; Ahnen, Dennis J; Sandler, Robert S; Lance, Peter; Stern, Mariana C

    2010-12-01

    A diet high in red meat is an established colorectal cancer (CRC) risk factor. Carcinogens generated during meat cooking have been implicated as causal agents and can induce oxidative DNA damage, which elicits repair by the base excision repair (BER) pathway. Using a family-based study, we investigated the role of polymorphisms in 4 BER genes (APEX1 Gln51His, Asp148Glu; OGG1 Ser236Cys; PARP Val742Ala; and XRCC1 Arg194Trp, Arg280His, Arg399Gln) as potential CRC risk factors and modifiers of the association between diets high in red meat or poultry and CRC risk. We tested for gene-environment interactions using case-only analyses (n = 577) and compared statistically significant results with those obtained using case-unaffected sibling comparisons (n = 307 sibships). Carriers of the APEX1 codon 51 Gln/His genotype had a reduced CRC risk compared with carriers of the Gln/Gln genotype (odds ratio (OR) = 0.15, 95% CI = 0.03-0.69, P = 0.015). The association between higher red meat intake (>3 servings per week) and CRC was modified by the PARP Val762Ala single-nucleotide polymorphisms (SNP; case-only interaction P = 0.026). This SNP also modified the association between higher intake of high-temperature cooked red meat (case-only interaction P = 0.0009). We report evidence that the BER pathway PARP gene modifies the association of diets high in red meat cooked at high temperatures with risk of CRC. Our findings suggest a contribution to colorectal carcinogenesis of free radical damage as one of the possible harmful effects of a diet high in red meat. ©2010 AACR.

  2. Lipman Bers, a life in mathematics

    CERN Document Server

    Keen, Linda; Rodríguez, Rubí E

    2015-01-01

    The book is part biography and part collection of mathematical essays that gives the reader a perspective on the evolution of an interesting mathematical life. It is all about Lipman Bers, a giant in the mathematical world who lived in turbulent and exciting times. It captures the essence of his mathematics, a development and transition from applied mathematics to complex analysis-quasiconformal mappings and moduli of Riemann surfaces-and the essence of his personality, a progression from a young revolutionary refugee to an elder statesman in the world of mathematics and a fighter for global h

  3. Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Cornish, Adam J.; Ginovska, Bojana; Thelen, Adam; da Silva, Julio C. S.; Soares, Thereza A.; Raugei, Simone; Dupuis, Michel; Shaw, Wendy J.; Hegg, Eric L.

    2016-06-07

    The proton pathway of [FeFe]-hydrogenase is essential for enzymatic H2 production and oxidation and is composed of four residues and a modeled water molecule. Recently, a computational analysis of this pathway revealed that the solvent-exposed residue of the pathway (Glu282) could form hydrogen bonds to two residues outside of the pathway (Arg286 and Ser320), implicating that these residues could function in regulating proton transfer. Substituting Arg286 with leucine eliminates hydrogen bonding with Glu282 and results in a 2.5-fold enhancement in H2 production activity, suggesting that Arg286 serves an important role in controlling the rate of proton delivery. In contrast, substitution of Ser320 with alanine reduces the rate approximately 5-fold, implying that it either acts as a member of the pathway or influences Glu282 to enable proton transfer. Interestingly, QM/MM and molecular dynamics calculations indicate that Ser320 does not play an electronic or structural role. QM calculations also estimate that including Ser320 in the pathway does not significantly change the barrier to proton movement, providing further support for its role as a member of the proton pathway. While further studies are needed to quantify the role of Ser320, collectively, these data provide evidence that the enzyme scaffold plays a significant role in modulating the activity of the enzyme, demonstrating that the rate of intraprotein proton transfer can be accelerated, particularly in a non-biological context. This work was supported by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science, DE-FC02-07ER64494). In addition, support from the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences (WJS, BGP, SR) is gratefully acknowledged. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of

  4. Paradigmenwechsel in der politischen Ökologie? Zur deutschen Diskussion über die Lokale Agenda 21

    OpenAIRE

    Pettenkofer, Andreas

    2001-01-01

    Der Text berichtet über die in Deutschland geführte sozialwissenschaftliche Diskussion über das umweltpolitische Programm Lokale Agenda 21; er versucht eine vorläufige Rekonstruktion der spezifischen Gestalt der Agenda-Prozesse und ihrer Abweichungen von der westdeutschen Tradition der Politischen Ökologie, und diskutiert die theoretischen Fragen, die sich angesichts dieser neuartigen Phänomene stellen. Dabei geht es vor allem um die Angemessenheit der modernisierungstheoretischen Perspektive...

  5. Modulation of guanosine nucleotides biosynthetic pathways enhanced GDP-L-fucose production in recombinant Escherichia coli.

    Science.gov (United States)

    Lee, Won-Heong; Shin, So-Yeon; Kim, Myoung-Dong; Han, Nam Soo; Seo, Jin-Ho

    2012-03-01

    Guanosine 5'-triphosphate (GTP) is the key substrate for biosynthesis of guanosine 5'-diphosphate (GDP)-L-fucose. In this study, improvement of GDP-L-fucose production was attempted by manipulating the biosynthetic pathway for guanosine nucleotides in recombinant Escherichia coli-producing GDP-L-fucose. The effects of overexpression of inosine 5'-monophosphate (IMP) dehydrogenase, guanosine 5'-monophosphate (GMP) synthetase (GuaB and GuaA), GMP reductase (GuaC) and guanosine-inosine kinase (Gsk) on GDP-L-fucose production were investigated in a series of fed-batch fermentations. Among the enzymes tested, overexpression of Gsk led to a significant improvement of GDP-L-fucose production. Maximum GDP-L-fucose concentration of 305.5 ± 5.3 mg l(-1) was obtained in the pH-stat fed-batch fermentation of recombinant E. coli-overexpressing Gsk, which corresponds to a 58% enhancement in the GDP-L-fucose production compared with the control strain overexpressing GDP-L-fucose biosynthetic enzymes. Such an enhancement of GDP-L-fucose production could be due to the increase in the intracellular level of GMP.

  6. Optical and magneto-optical effects in Hg{sub 1-x}Cd{sub x}Cr{sub 2}Se{sub 4} (0 ⩽ x ⩽ 1) single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Sukhorukov, Yu. P., E-mail: suhorukov@imp.uran.ru; Telegin, A. V.; Bebenin, N. G.; Zainullina, R. I.; Mostovshchikova, E. V.; Viglin, N. A. [Ural Branch, Russian Academy of Sciences, Mikheev Institute of Metal Physics (Russian Federation); Gan’shina, E. A.; Zykov, G. S. [Moscow State University (Russian Federation); Fedorov, V. A. [Russian Academy of Sciences, Kurnakov Institute of Inorganic Chemistry (Russian Federation); Menshchikova, T. K.; Buchkevich, A. A. [Ural Branch, Russian Academy of Sciences, Mikheev Institute of Metal Physics (Russian Federation)

    2015-09-15

    The concentration, temperature, and magnetic-field dependences of the magnetoreflection and magnetotransmission of natural light in the infrared spectral range and the Kerr effect in single crystals of ferromagnetic Hg{sub 1-x}Cd{sub x}Cr{sub 2}Se{sub 4} (0 ⩽ x ⩽ 1) spinels have been studied. A relationship of the magneto-optical properties to the electronic band structure of spinels has been established. The most significant changes in the spectra of magnetoreflection, magnetotransmission, and the Kerr effect are shown to be observed for 0.1 < x < 0.25 and are attributable to a rearrangement of the band structure as the composition changes.

  7. Unusually high critical current of P-doped BaFe{sub 2}As{sub 2} single crystalline thin film

    Energy Technology Data Exchange (ETDEWEB)

    Kurth, Fritz; Engelmann, Jan; Schultz, Ludwig [IMW, IFW Dresden, Dresden (Germany); TU Dresden, Dresden (Germany); Tarantini, Chiara; Jaroszynski, Jan [ASC, NHMFL, Florida (United States); Grinenko, Vadim; Reich, Elke; Huehne, Ruben [IMW, IFW Dresden, Dresden (Germany); Haenisch, Jens [IMW, IFW Dresden, Dresden (Germany); ITEP, KIT, Karlsruhe (Germany); Mori, Yasohiro; Sakagami, Akihiro; Kawaguchi, Takahiko; Ikuta, Hiroshi [Department of Crystalline Materials Science, Nagoya University, Nagoya (Japan); Holzapfel, Bernhard [ITEP, KIT, Karlsruhe (Germany); Iida, Kazumasa [IMW, IFW Dresden, Dresden (Germany); Department of Crystalline Materials Science, Nagoya University, Nagoya (Japan)

    2015-07-01

    Microstructurally clean, isovalently P-doped BaFe{sub 2}As{sub 2} single crystalline thin films have been prepared by molecular beam epitaxy. These films show a superconducting transition temperature (T{sub c}) of over 30 K and high transport self-field critical current densities (J{sub c}) of over 6 MA/cm{sup 2} at 4.2 K, which are among the highest for Fe based superconductors. In-field J{sub c} exceeds 0.1 MA/cm{sup 2} at μ{sub 0}H = 35 T for H parallel ab and μ{sub 0}H = 18 T for H parallel c, respectively, in spite of moderate upper critical fields compared to other FeSCs with similar T{sub c}. This unusually high J{sub c} makes P-doped Ba-122 very favorable for high-field magnet applications.

  8. Hierarchical domain structure of lead-free piezoelectric (Na{sub 1/2} Bi{sub 1/2})TiO{sub 3}-(K{sub 1/2} Bi{sub 1/2})TiO{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Chengtao, E-mail: lchentao@vt.edu; Wang, Yaojin; Ge, Wenwei; Li, Jiefang; Viehland, Dwight [Materials Science and Engineering, Virginia Tech, Blacksburg, Virginia 24061 (United States); Delaire, Olivier [Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Li, Xiaobin; Luo, Haosu [Shanghai Institute of Ceramics, Chinese Academy of Sciences, 215 Chengbei Road, Jiading, Shanghai 201800 (China)

    2016-05-07

    We report a unique hierarchical domain structure in single crystals of (Na{sub 1/2}Bi{sub 1/2})TiO{sub 3}-xat. %(K{sub 1/2}Bi{sub 1/2})TiO{sub 3} for x = 5 and 8 by transmission electron microscopy (TEM). A high density of polar nano-domains with a lamellar morphology was found, which were self-assembled into a quadrant-like configuration, which then assembled into conventional ferroelectric macro-domains. Studies by high resolution TEM revealed that the polar lamellar regions contained a coexistence of in-phase and anti-phase oxygen octahedral tilt regions of a few nanometers in size. Domain frustration over multiple length scales may play an important role in the stabilization of the hierarchy, and in reducing the piezoelectric response of this Pb-free piezoelectric solid solution.

  9. Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes.

    Directory of Open Access Journals (Sweden)

    Claire Chewapreecha

    2014-08-01

    Full Text Available Traditional genetic association studies are very difficult in bacteria, as the generally limited recombination leads to large linked haplotype blocks, confounding the identification of causative variants. Beta-lactam antibiotic resistance in Streptococcus pneumoniae arises readily as the bacteria can quickly incorporate DNA fragments encompassing variants that make the transformed strains resistant. However, the causative mutations themselves are embedded within larger recombined blocks, and previous studies have only analysed a limited number of isolates, leading to the description of "mosaic genes" as being responsible for resistance. By comparing a large number of genomes of beta-lactam susceptible and non-susceptible strains, the high frequency of recombination should break up these haplotype blocks and allow the use of genetic association approaches to identify individual causative variants. Here, we performed a genome-wide association study to identify single nucleotide polymorphisms (SNPs and indels that could confer beta-lactam non-susceptibility using 3,085 Thai and 616 USA pneumococcal isolates as independent datasets for the variant discovery. The large sample sizes allowed us to narrow the source of beta-lactam non-susceptibility from long recombinant fragments down to much smaller loci comprised of discrete or linked SNPs. While some loci appear to be universal resistance determinants, contributing equally to non-susceptibility for at least two classes of beta-lactam antibiotics, some play a larger role in resistance to particular antibiotics. All of the identified loci have a highly non-uniform distribution in the populations. They are enriched not only in vaccine-targeted, but also non-vaccine-targeted lineages, which may raise clinical concerns. Identification of single nucleotide polymorphisms underlying resistance will be essential for future use of genome sequencing to predict antibiotic sensitivity in clinical microbiology.

  10. Luminescent, optical and electronic properties of La{sub 3}Ta{sub 0.5}Ga{sub 5.5}O{sub 14} single crystals grown in different atmospheres

    Energy Technology Data Exchange (ETDEWEB)

    Spassky, D.A., E-mail: deris2002@mail.ru [National University of Science and Technology (MISiS), Leninsky Prospekt, 4, Moscow 119049 (Russian Federation); Institute of Physics, University of Tartu, Ravila 14c, Tartu 50411 (Estonia); Skobeltsyn Institute of Nuclear Physics, M.V. Lomonosov Moscow State University, 119991 Moscow (Russian Federation); Brik, M.G. [Institute of Physics, University of Tartu, Ravila 14c, Tartu 50411 (Estonia); College of Sciences, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China); Institute of Physics, Jan Dlugosz University, Armii Krajowej 13/15, PL-42200 Czestochowa (Poland); Kozlova, N.S.; Kozlova, A.P.; Zabelina, E.V. [National University of Science and Technology (MISiS), Leninsky Prospekt, 4, Moscow 119049 (Russian Federation); Buzanov, O.A. [Fomos-Materials, Buzheninova 16, Moscow 107023 (Russian Federation); Belsky, A. [Institute of Light and Matter, CNRS, University Lyon1, Villeurbanne 69622 (France)

    2016-09-15

    Luminescent, optical and electronic properties of La{sub 3}Ta{sub 0.5}Ga{sub 5.5}O{sub 14} single crystals grown in different atmospheres are presented. The absorption bands at 255, 290, 350 and 480 nm were detected; the intensity of bands increases with the concentration of oxygen in the growth atmosphere. It is shown that the shift of the fundamental absorption edge with the temperature obeys Urbach rule. The corresponding fitting allowed to estimate the slope coefficient σ=0.35, which implies self-trapping of excitons in La{sub 3}Ta{sub 0.5}Ga{sub 5.5}O{sub 14}. Calculations of the band structure, partial densities of states and reflectivity spectra were performed. The bandgap of La{sub 3}Ta{sub 0.5}Ga{sub 5.5}O{sub 14} was determined as E{sub g}=5.6 eV. The luminescence properties under UV, VUV and X-ray excitation were studied. Intrinsic emission band at 440–450 nm is attributed to the excitons self-trapped at TaO{sub 6} molecular complexes. Extrinsic emission bands at 410, 440 and 550 nm are attributed to the emission of excitons trapped by antisite defects, F-centers and oxygen deficient oxyanionic complexes.

  11. Das Volkslied in Deutschland, Frankreich, Belgien und Holland. Untersuchungen über die Auffassung des Begriffes; Über die traditionellen Zeilen, die Zahlen-, Blumen- und Farbensymbolik

    NARCIS (Netherlands)

    Brouwer, Cornelis

    1930-01-01

    Wenn man die gewaltige Menge Publikationen über das Volkslied, die im Laufe des 19. und 20. Jahrhunderts in Deutschland, Frankreich, Belgien und Holland erschienen sind, vergleicht, springen zwei Punkte sofort ins Auge: 1. der Unterschied zwischen den verschiedenen Auffassungen vom Begriff Volkslied

  12. Single nucleotide polymorphism analysis of ubiquitin extension protein genes (ubq) of gossypium arboreum and gossypium herbaceum in comparison with arabidopsis thaliana

    International Nuclear Information System (INIS)

    Shaheen, T.; Zafar, Y.; Rahman, M.

    2014-01-01

    Single nucleotide polymorphism analysis is an expedient way to study polymorphisms at genomic level. In the present study we have explored Ubiquitin extension protein gene of G. arboreum (A2) and G. herbaceum (A1) of cotton which is a multiple copy gene. We have found SNPs at 16 positions in 200 bp region within A genome of cotton indicating frequency of SNPs 1/13 bp. Both sequences from cotton have shown maximum similarity with UBQ5 and UBQ6 of Arabidopsis thaliana. Sequence obtained from G. arboreum has shown SNPs at 28 positions in comparison with each UBQ5 and UBQ6 of Arabidopsis thaliana while sequence obtained from G. herbaceum has shown SNPs at 31 positions in comparison with each UBQ5 and UBQ6 of Arabidopsis thaliana. In conclusion although during pace of evolution ubiquitin extension protein genes of both A genome species have got some mutations from nature but still most of their sequence is similar. Single nucleotide polymorphism study can prove a vital tool to identify gene type in case of Multicopy genes. (author)

  13. Two gap superconductivity in Ba{sub 0.55}K{sub 0.45}Fe{sub 2}As{sub 2} single crystals studied by the directional point-contact Andreev reflection spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Szabo, P.; Pribulova, Z. [Centre of Low Temperature Physics, IEP Slovak Academy of Sciences and P.J.Safarik University, Watsonova 47, SK-04001 Kosice (Slovakia); Pristas, G.; Bud' ko, S.L.; Canfield, P.C. [Ames Laboratory and Iowa State University, Ames, IA 50011 (United States); Samuely, P., E-mail: samuely@saske.s [Centre of Low Temperature Physics, IEP Slovak Academy of Sciences and P.J.Safarik University, Watsonova 47, SK-04001 Kosice (Slovakia)

    2009-10-15

    First directional point-contact Andreev reflection spectroscopy on the Ba{sub 0.55}K{sub 0.45}Fe{sub 2}As{sub 2} single crystals is presented. The spectra show significant differences when measured in the ab plane in comparison with those measured in the c direction. In the latter case no traces of superconducting energy gap could be found, just a reduced point-contact conductance persisting up to about 100 K and indicating reduced density of states. On the other hand within the ab plane two nodeless superconducting energy gaps DELTA{sub S}approx2-5 meV and DELTA{sub L}approx9-11 meV are detected.

  14. Notizen über Thatcheria Angas, Clinura Bellardi und Clinuropsis Vincent

    NARCIS (Netherlands)

    Beets, C.

    1942-01-01

    1. Es sind bisher über die merkwürdige rezente marine Gastropoden-Gruppe Thatcheria Angas, 1877 sehr wenige Gegebenheiten bekannt, vergleichende Untersuchungen mit fossilen Arten fehlen (fast) vollkommen und auch die Frage ihrer systematischen Stellung ist nie in befriedigender Weise gelöst worden.

  15. Growth and spectroscopic properties of Yb{sup 3+}-doped Li{sub 6}Y(BO{sub 3}){sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Brenier, A. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France)]. E-mail: brenier@pcml.univ-lyon1.fr; Yoshikawa, A. [Institute of Multidisciplinary for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan); Lebbou, K. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France); Jouini, A. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France); Institute of Multidisciplinary for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan); Aloui-Lebbou, O. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France); Boulon, G. [Laboratoire de Physico-Chimie des Materiaux Luminescents, UMR CNRS no 5620, Universite Claude Bernard-Lyon1, 10 rue Ampere, 69622 Villeurbanne (France); Institute of Multidisciplinary for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan); Fukuda, T. [Institute of Multidisciplinary for Advanced Materials, Tohoku University, Sendai 980 8577 (Japan)

    2007-10-15

    The spectroscopic properties of high-quality Czochralski grown 20% Yb{sup 3+}-doped Li{sub 6}Y(BO{sub 3}){sub 3} single crystal as new promising laser material are presented. The crystal was seeded-grown in the <0 1 0> direction and its crystallinity was measured using X-ray rocking curve analysis. Low temperature transmission spectrum exhibits broad bands in a short range of wavelengths and two sharp lines at 972.5 and 978 nm, interpreted as two zero-lines of two nonequivalent Yb{sup 3+} centers inside the lattice. The fluorescence lifetimes associated to these two intense lines are different: 0.867 and 1.33 ms. An attempt of determination of the Stark sublevels energies of the {sup 4}F{sub 5/2} and {sup 4}F{sub 7/2} manifolds of the two Yb{sup 3+} nonequivalent ions is given. The polarized absorption and emission spectra were also recorded at room temperature and we conclude that the most favorable emission line for laser application could be around 1042 nm in n {sub g} polarization.

  16. Luminescent and scintillation properties of Bi{sup 3+} doped Y{sub 2}SiO{sub 5} and Lu{sub 2}SiO{sub 5} single crystalline films

    Energy Technology Data Exchange (ETDEWEB)

    Zorenko, Yu., E-mail: zorenko@ukw.edu.pl [Institute of Physics, Kazimierz Wielki University in Bydgoszcz, 85-090 Bydgoszcz (Poland); Gorbenko, V.; Zorenko, T. [Institute of Physics, Kazimierz Wielki University in Bydgoszcz, 85-090 Bydgoszcz (Poland); Laboratory for Optoelectronic Materials (LOM), Department of Electronics of Ivan Franko National University of Lviv, 79017 Lviv (Ukraine); Malinowski, P. [Institute of Physics, Kazimierz Wielki University in Bydgoszcz, 85-090 Bydgoszcz (Poland); Jary, V.; Kucerkova, R.; Beitlerova, A.; Mares, J.A.; Nikl, M. [Institute of Physics AS CR, Cukrovarnicka 10, 16253 Prague (Czech Republic); Fedorov, A. [Institute for Single Crystals NAS of Ukraine, 60 Lenin ave., 61001 Kharkiv (Ukraine)

    2014-10-15

    In this paper we report our follow-up research on the Bi{sup 3+} luminescence in orthosilicate compounds, focusing on absorption, luminescent and scintillation properties of YSO:Bi and LSO:Bi SCFs with the Bi concentration ranging from 0.05 to 0.18 at%. For purpose of this research, single crystalline films (SCF) of Y{sub 2}SiO{sub 5}:Bi and Lu{sub 2}SiO{sub 5}:Bi have been grown by the LPE method onto YSO and LSO substrates from the melt-solution based on Bi{sub 2}O{sub 3} flux. - Highlights: • YSO:Bi and LSO:Bi films have been grown by liquid phase epitaxy. • Bi{sup 3+} absorption and luminescence depends on Bi concentration. • Scintillation properties of YSO:Bi and LSO:Bi films have been studied.

  17. Sequencing genes in silico using single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Zhang Xinyi

    2012-01-01

    Full Text Available Abstract Background The advent of high throughput sequencing technology has enabled the 1000 Genomes Project Pilot 3 to generate complete sequence data for more than 906 genes and 8,140 exons representing 697 subjects. The 1000 Genomes database provides a critical opportunity for further interpreting disease associations with single nucleotide polymorphisms (SNPs discovered from genetic association studies. Currently, direct sequencing of candidate genes or regions on a large number of subjects remains both cost- and time-prohibitive. Results To accelerate the translation from discovery to functional studies, we propose an in silico gene sequencing method (ISS, which predicts phased sequences of intragenic regions, using SNPs. The key underlying idea of our method is to infer diploid sequences (a pair of phased sequences/alleles at every functional locus utilizing the deep sequencing data from the 1000 Genomes Project and SNP data from the HapMap Project, and to build prediction models using flanking SNPs. Using this method, we have developed a database of prediction models for 611 known genes. Sequence prediction accuracy for these genes is 96.26% on average (ranges 79%-100%. This database of prediction models can be enhanced and scaled up to include new genes as the 1000 Genomes Project sequences additional genes on additional individuals. Applying our predictive model for the KCNJ11 gene to the Wellcome Trust Case Control Consortium (WTCCC Type 2 diabetes cohort, we demonstrate how the prediction of phased sequences inferred from GWAS SNP genotype data can be used to facilitate interpretation and identify a probable functional mechanism such as protein changes. Conclusions Prior to the general availability of routine sequencing of all subjects, the ISS method proposed here provides a time- and cost-effective approach to broadening the characterization of disease associated SNPs and regions, and facilitating the prioritization of candidate

  18. Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process

    DEFF Research Database (Denmark)

    Ramírez-Soriano, Anna; Nielsen, Rasmus

    2009-01-01

    Most single-nucleotide polymorphism (SNP) data suffer from an ascertainment bias caused by the process of SNP discovery followed by SNP genotyping. The final genotyped data are biased toward an excess of common alleles compared to directly sequenced data, making standard genetic methods of analysis...... the variances and covariances of these estimators and provide a corrected version of Tajima's D statistic. We reanalyze a human genomewide SNP data set and find substantial differences in the results with or without ascertainment bias correction....

  19. A-Site Cation Substitutions in Strained Y-Doped BaZrO<sub>3sub> Multilayer Films Leading to Fast Proton Transport Pathways

    Energy Technology Data Exchange (ETDEWEB)

    Aruta, Carmela [Univ. of Roma Tor Vergata, Rome (Italy); Han, Chu [Georgia Inst. of Technology, Atlanta, GA (United States); Zhou, Si [Dalian Univ. of Technology, Dalian (China); Cantoni, Claudia [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Yang, Nan [Univ. of Roma Tor Vergata, Rome (Italy); Tebano, Antonello [Univ. of Roma Tor Vergata, Rome (Italy); Lee, Tien -Lin [Diamond Light Source Ltd., Didcot (United Kingdom); Schlueter, Christoph [Diamond Light Source Ltd., Didcot (United Kingdom); Bongiorno, Angelo [College of Staten Island, Staten Island, NY (United States); The Graduate Center of the City Univ. of New York, New York, NY (United States)

    2016-03-31

    Proton-conducting perovskite oxides form a class of solid electrolytes for novel electrochemical devices operating at moderate temperatures. Here, we use hard X-ray photoelectron spectroscopy, scanning transmission electron microscopy, and density functional theory calculations to investigate the structure and elucidate the origin of the fast proton transport properties of strained ultrathin films of Y-doped BaZrO<sub>3sub> grown by pulsed lased deposition on NdGaO<sub>3sub>. Our study shows that our BaZr<sub>0.8sub>Y>0.2sub>O>3sub> films incorporate a significant amount of Y dopants, and to a lesser extent also Zr ions, substituting for Ba2+, and that these substitutional defects agglomerate forming columnar regions crossing vertically from the surface to the interface the entire film. In conclusion, our calculations also show that, in regions rich in Y substitutions for both Zr and Ba, the proton transfer process involves nearly zero-energy barriers, indicating that A-site cation substitutions by Y lead to fast transport pathways and hence are responsible for the previously observed enhanced values of the proton conductivity of these perovskite oxide films.

  20. Crystal structure of the β<sub>2sub> adrenergic receptor-Gs protein complex

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, Søren G.F.; DeVree, Brian T; Zou, Yaozhong; Kruse, Andrew C; Chung, Ka Young; Kobilka, Tong Sun; Thian, Foon Sun; Chae, Pil Seok; Pardon, Els; Calinski, Diane; Mathiesen, Jesper M; Shah, Syed T.A.; Lyons, Joseph A; Caffrey, Martin; Gellman, Samuel H; Steyaert, Jan; Skiniotis, Georgios; Weis, William I; Sunahara, Roger K; Kobilka, Brian K [Brussels; (Trinity); (Michigan); (Stanford-MED); (Michigan-Med); (UW)

    2011-12-07

    G protein-coupled receptors (GPCRs) are responsible for the majority of cellular responses to hormones and neurotransmitters as well as the senses of sight, olfaction and taste. The paradigm of GPCR signalling is the activation of a heterotrimeric GTP binding protein (G protein) by an agonist-occupied receptor. The β<sub>2sub> adrenergic receptor (β<sub>2sub>AR) activation of Gs, the stimulatory G protein for adenylyl cyclase, has long been a model system for GPCR signalling. Here we present the crystal structure of the active state ternary complex composed of agonist-occupied monomeric β<sub>2sub>AR and nucleotide-free Gs heterotrimer. The principal interactions between the β<sub>2sub>AR and Gs involve the amino- and carboxy-terminal α-helices of Gs, with conformational changes propagating to the nucleotide-binding pocket. The largest conformational changes in the β<sub>2sub>AR include a 14Å outward movement at the cytoplasmic end of transmembrane segment 6 (TM6) and an α-helical extension of the cytoplasmic end of TM5. The most surprising observation is a major displacement of the α-helical domain of Gαs relative to the Ras-like GTPase domain. This crystal structure represents the first high-resolution view of transmembrane signalling by a GPCR.

  1. Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

    Directory of Open Access Journals (Sweden)

    Arnett Donna

    2009-08-01

    Full Text Available Abstract Background Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST can evidence environmental selection pressures. Such genetic information is limited in Puerto Ricans, the second largest Hispanic ethnic group in the US, and a group with high prevalence of chronic disease. We determined allele frequencies and population differentiation for 101 single nucleotide polymorphisms (SNPs in 30 genes involved in major metabolic and disease-relevant pathways in Puerto Ricans (n = 969, ages 45–75 years and compared them to similarly aged non-Hispanic whites (NHW (n = 597. Results Minor allele frequency (MAF distributions for 45.5% of the SNPs assessed in Puerto Ricans were significantly different from those of NHW. Puerto Ricans carried risk alleles in higher frequency and protective alleles in lower frequency than NHW. Patterns of population differentiation showed that Puerto Ricans had SNPs with exceptional FST values in intronic, non-synonymous and promoter regions. NHW had exceptional FST values in intronic and promoter region SNPs only. Conclusion These observations may serve to explain and broaden studies on the impact of gene polymorphisms on chronic diseases affecting Puerto Ricans.

  2. IL10 single nucleotide polymorphisms are related to upregulation of constitutive IL-10 production and susceptibility to Helicobacter pylori infection.

    Science.gov (United States)

    Assis, Shirleide; Marques, Cintia Rodrigues; Silva, Thiago Magalhães; Costa, Ryan Santos; Alcantara-Neves, Neuza Maria; Barreto, Mauricio Lima; Barnes, Kathleen Carole; Figueiredo, Camila Alexandrina

    2014-06-01

    Helicobacter pylori infection is a strong risk factor for gastric cancer, likely due to the extensive inflammation in the stomach mucosa caused by these bacteria. Many studies have reported an association between IL10 polymorphisms, the risk of gastric cancer, and IL-10 production. The aim of the study was to evaluate the association between IL10 genetic variants, Helicobacter pylori infection, and IL-10 production by peripheral blood leukocytes in children. We genotyped a total of 12 single nucleotide polymorphisms in IL10 in 1259 children aged 4-11 years living in a poor urban area in Salvador, Brazil, using TaqMan probe based, 5' nuclease assay minor groove binder chemistry. Association tests were performed by logistic regression for Helicobacter pylori infection and linear regression for IL-10 spontaneous production (whole-blood cultures) including sex, age, and principal components for informative ancestry markers as covariates, using PLINK. Our results shown that IL10 single nucleotide polymorphisms rs1800896 (OR = 1.63; 95% CI = 1.11-2.39), rs3024491 (OR = 1.71; 95% CI = 1.14-2.57), rs1878672 (OR = 1.79; 95% CI = 1.19-2.68), and rs3024496 (OR = 1.48; 95% CI = 1.05-2.08) were positively associated with Helicobacter pylori infection. Eight single nucleotide polymorphisms were associated with spontaneous production of IL-10 in culture, of which three (rs1800896 and rs1878672, p = .04; rs3024491, p = .01) were strongly associated with infection by Helicobacter pylori. Our results indicate that IL10 variants rs1800896, rs3024491, rs1878672, and rs3024496 are more consistently associated with the presence of anti-H. pylori IgG by inducing increased production of IL-10. Further studies are underway to elucidate the role of additional genetic variants and to investigate their impact on the occurrence of gastric cancer. © 2014 John Wiley & Sons Ltd.

  3. Luminescence investigation of Yb{sup 3+}/Er{sup 3+} codoped single LiYF{sub 4} microparticle

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Wei; Zheng, Hairong, E-mail: hrzheng@snnu.edu.cn; He, Enjie; Lu, Ying; Gao, Fangqi

    2014-08-01

    Tetragonal phase LiYF{sub 4}:Yb{sup 3+}/Er{sup 3+} microparticles are synthesized via facile hydrothermal method. Single LiYF{sub 4} microparticle is excited with IR laser at 980 nm in a confocal setup, and strong green and weak red emissions are observed. It is found that single LiYF{sub 4}:Yb{sup 3+}/Er{sup 3+} microparticle with sub-structure presents stronger upconversion luminescence emission and smaller intensity ratio of red to green emission than that from LiYF{sub 4}:Yb{sup 3+}/Er{sup 3+} microparticle with no sub-structure. The possible mechanism, the influence of particle size and the existence of EDTA on the upconversion luminescence emission are investigated. The current study suggests that the luminescence observation with single micropaticle can effectively avoid the influence of environment and neighbor particles, which is important for investigating the luminescence properties of micro- or nano-crystals and for extending their application. - Highlights: • Single LiYF{sub 4} microparticle is excited with IR laser at 980 nm in a confocal setup, and strong green and weak red emissions are observed. • Single LiYF{sub 4} microparticle with different morphology exhibits different fluorescence emission intensity and intensity ratio of red to green emission. • The possible mechanism, the influence of particle size and the existence of EDTA on the upconversion emission are investigated.

  4. Surface texture of single-crystal silicon oxidized under a thin V{sub 2}O{sub 5} layer

    Energy Technology Data Exchange (ETDEWEB)

    Nikitin, S. E., E-mail: nikitin@mail.ioffe.ru; Verbitskiy, V. N.; Nashchekin, A. V.; Trapeznikova, I. N.; Bobyl, A. V.; Terukova, E. E. [Russian Academy of Sciences, Ioffe Physical–Technical Institute (Russian Federation)

    2017-01-15

    The process of surface texturing of single-crystal silicon oxidized under a V{sub 2}O{sub 5} layer is studied. Intense silicon oxidation at the Si–V{sub 2}O{sub 5} interface begins at a temperature of 903 K which is 200 K below than upon silicon thermal oxidation in an oxygen atmosphere. A silicon dioxide layer 30–50 nm thick with SiO{sub 2} inclusions in silicon depth up to 400 nm is formed at the V{sub 2}O{sub 5}–Si interface. The diffusion coefficient of atomic oxygen through the silicon-dioxide layer at 903 K is determined (D ≥ 2 × 10{sup –15} cm{sup 2} s{sup –1}). A model of low-temperature silicon oxidation, based on atomic oxygen diffusion from V{sub 2}O{sub 5} through the SiO{sub 2} layer to silicon, and SiO{sub x} precipitate formation in silicon is proposed. After removing the V{sub 2}O{sub 5} and silicon-dioxide layers, texture is formed on the silicon surface, which intensely scatters light in the wavelength range of 300–550 nm and is important in the texturing of the front and rear surfaces of solar cells.

  5. Single-layer and double-layer microwave absorbers based on Co{sub 67}Ni{sub 33} microspheres and Ni{sub 0.6}Zn{sub 0.4}Fe{sub 2}O{sub 4} nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Min [Engineering Technology Research Center of Magnetic Materials of Anhui Province, School of Physics & Materials Science, Anhui University, Hefei 230601 (China); Wang, Zhongzhu, E-mail: wangzz@ahu.edu.cn [Engineering Technology Research Center of Magnetic Materials of Anhui Province, School of Physics & Materials Science, Anhui University, Hefei 230601 (China); Wang, Peihong; Liao, Yanlin [Engineering Technology Research Center of Magnetic Materials of Anhui Province, School of Physics & Materials Science, Anhui University, Hefei 230601 (China); Bi, Hong [School of Chemistry and Chemical Engineering, Anhui University, Hefei 230601 (China)

    2017-03-01

    Co{sub 67}Ni{sub 33} microspheres and Ni{sub 0.6}Zn{sub 0.4}Fe{sub 2}O{sub 4} nanocrystals were synthesized by hydrothermal method. The complex permeability and complex permittivity of the as-prepared powders dispersing in wax (60 wt% powder) were measured using a vector network analyzer in 2–18 GHz frequency range. The calculated microwave absorption of single-layer and double-layer absorbers based on Co{sub 67}Ni{sub 33} microspheres and Ni{sub 0.6}Zn{sub 0.4}Fe{sub 2}O{sub 4} nanocrystals were analyzed in 2–18 GHz frequency range. The results show that the Ni{sub 0.6}Zn{sub 0.4}Fe{sub 2}O{sub 4}nanocrystals with the relatively low permittivity and Co{sub 67}Ni{sub 33} microspheres with the relatively high dielectric loss and magnetic loss can be used as proper matching layer and excellent absorption layer, respectively. The double-layer absorber with a coating thickness of 2.1 mm exhibits a maximum reflection loss of −43.8 dB as well as a bandwidth (reflection loss less than −10 dB) of 5 GHz. Moreover, their absorption peak and the absorption intensity can be adjusted easily through changing the stacking order and each layer thickness. - Highlights: • Ni-Zn ferrite nanocrystals can use as matching layer in double-layer absorbers. • Co{sub 67}Ni{sub 33} microspheres with high dielectric loss can use as absorption layer. • Double-layer absorbers exhibits an excellent microwave absorption in 2–18 GHz.

  6. Universal behavior of magnetocaloric effect in a layered perovskite La{sub 1.2}Sr{sub 1.8}Mn{sub 2}O{sub 7} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Thanh, Tran Dang, E-mail: thanhxraylab@yahoo.com [Institute of Materials Science, Vietnam Academy of Science and Technology, 18-Hoang Quoc Viet, Hanoi (Viet Nam); Manh, T.V.; Ho, T.A. [Department of Physics, Chungbuk National University, Cheongju 361-763 (Korea, Republic of); Telegin, Andrey [Department of Magnetic Semiconductors, Institute of Metal Physics, RAS (Russian Federation); Phan, T.L. [Department of Physics and Oxide Research Center, Hankuk University of Foreign Studies, Yongin 449-791 (Korea, Republic of); Yu, S.C., E-mail: scyu@chungbuk.ac.kr [Department of Physics, Chungbuk National University, Cheongju 361-763 (Korea, Republic of)

    2016-04-01

    In this paper, we present a detailed analysis on temperature and magnetic field dependences of the magnetic entropy change (ΔS{sub m}) near the ferromagnetic (FM)–paramagnetic (PM) phase transition of a La{sub 1.2}Sr{sub 1.8}Mn{sub 2}O{sub 7} single crystal. Experimental results reveal the material exhibiting a FM–PM phase transition at T{sub C}=85 K, and belongs to a second-order phase transition (SOPT). Around T{sub C}, −ΔS{sub m} reaches the maximum value (|ΔS{sub max}|), which increases with increasing an applied magnetic field change, ΔH. The |ΔS{sub max}| values found are about 0.93, 1.73, 2.38, 2.91, and 3.33 J kg{sup −1} K{sup −1} for ΔH=10, 20, 30, 40, and 50 kOe, respectively. However, the peak position of the −ΔS{sub m}(T) curves is effectively shifted to higher temperatures when ΔH increases. Additionally, the ΔS{sub m}(T) curves measured at different ΔH values do not collapse into a universal curve when they are normalized to their respective ΔS{sub max} value, and Prod. Type: rescaled the temperature axis with θ{sub 1}=(T−T{sub C})/(T{sub r}−T{sub C}) for a reference temperature T{sub r}>T{sub C} or T{sub r}sub C}. Nevertheless, they can be collapsed into a unique curve in the whole temperature range if using two separated reference temperatures, T{sub r1} and T{sub r2}, with θ{sub 2}=−(T−T{sub C})/(T{sub r1}−T{sub C}) for T≤T{sub C} and θ{sub 2}=(T−T{sub C})/(T{sub r2}−T{sub C}) for T>T{sub C}.

  7. Evidence for the quasi-two dimensional behavior of the vortex structure in Bi[sub 2]Sr[sub 2]CaCu[sub 2]O[sub 8] single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Pastoriza, H [Comision Nacional de Energia Atomica, Centro Atomico Bariloche (Argentina); Arribere, A [Comision Nacional de Energia Atomica, Centro Atomico Bariloche (Argentina); Goffman, M F [Comision Nacional de Energia Atomica, Centro Atomico Bariloche (Argentina); Cruz, F de la [Comision Nacional de Energia Atomica, Centro Atomico Bariloche (Argentina); Mitzi, D B [Dept. of Applied Physics, Stanford Univ., CA (United States); Kapitulnik, A [Dept. of Applied Physics, Stanford Univ., CA (United States)

    1994-02-01

    AC susceptibility and dc magnetization measurements on Bi[sub 2]Sr[sub 2]CaCu[sub 2]O[sub 8] (BSCCO) single crystals in a wide range of temperatures clearly show that below the dc irreversibility line the vortex system loss the long range order in the c direction. The susceptibility data taken at 7 Hz show the different nature of two dissipation peaks: One related to the interplane currents at temperatures well below the dc irreversibility line and the other associated with the intraplane ones at temperatures above that line. In this sense the irreversibility line corresponds to the temperature where quasi-two dimensional vortices are depinned. (orig.)

  8. Luminescence and scintillation timing characteristics of (Lu{sub x}Gd{sub 2−x})SiO{sub 5}:Ce single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Yawai, Nattasuda; Chewpraditkul, Warut; Sakthong, Ongsa [Faculty of Science, King Mongkut' s University of Technology Thonburi, Bangkok10140 (Thailand); Chewpraditkul, Weerapong, E-mail: weerapong.che@kmutt.ac.th [Faculty of Science, King Mongkut' s University of Technology Thonburi, Bangkok10140 (Thailand); Wantong, Kriangkrai [Faculty of Science, King Mongkut' s University of Technology Thonburi, Bangkok10140 (Thailand); Szczesniak, Tomasz; Swiderski, Lukasz; Moszynski, Marek [National Centre for Nuclear Research, A. Soltana 7, PL 05-400 Otwock-Swierk (Poland); Sidletskiy, Oleg [Institute for Scintillation Materials NAS of Ukraine, 60 Nauky Avenue, 61001 Kharkiv (Ukraine)

    2017-02-01

    The luminescence and scintillation characteristics of cerium-doped lutetium-gadolinium orthosilicate (Lu{sub x}Gd{sub 2−x}SiO{sub 5}:Ce; x=0, 0.8, 1.8) single crystals were investigated. At 662 keV γ-rays, the light yield of 29,800±3000 ph MeV{sup −1} obtained for Lu{sub 1.8}Gd{sub 0.2}SiO{sub 5}:Ce is higher than that of 20,200±2000 and 11,800±1200 ph MeV{sup −1} obtained for Lu{sub 0.8}Gd{sub 1.2}SiO{sub 5}:Ce and Gd{sub 2}SiO{sub 5}:Ce, respectively. The fast component decay time of 32, 18 and 17 ns was measured in the scintillation decay of Gd{sub 2}SiO{sub 5}:Ce, Lu{sub 0.8}Gd{sub 1.2}SiO{sub 5}:Ce and Lu{sub 1.8}Gd{sub 0.2}SiO{sub 5}:Ce, respectively. The coincidence time spectra for 511 keV annihilation quanta were measured in reference to a fast BaF{sub 2} detector and time resolution was discussed in terms of a number of photoelectrons and decay time of the fast component. The mass attenuation coefficient for studied crystals at 60 and 662 keV γ-rays was also evaluated and discussed. - Highlights: • Scintillation timing characteristics of Lu{sub x}Gd{sub 2−x}SiO{sub 5}:Ce crystals are studied. • Lu{sub 1.8}Gd{sub 0.2}SiO{sub 5}:Ce exhibits excellent light yield and timing response. • Energy resolution of 6% @662 keV is obtained for Lu{sub 0.8}Gd{sub 1.2}SiO{sub 5}:Ce. • Coincidence time resolution of 368 ps is obtained for Lu{sub 1.8}Gd{sub 0.2}SiO{sub 5}:Ce.

  9. Association of prediabetes-associated single nucleotide polymorphisms with microalbuminuria.

    Science.gov (United States)

    Choi, Jong Wook; Moon, Shinje; Jang, Eun Jung; Lee, Chang Hwa; Park, Joon-Sung

    2017-01-01

    Increased glycemic exposure, even below the diagnostic criteria for diabetes mellitus, is crucial in the pathogenesis of diabetic microvascular complications represented by microalbuminuria. Nonetheless, there is limited evidence regarding which single nucleotide polymorphisms (SNPs) are associated with prediabetes and whether genetic predisposition to prediabetes is related to microalbuminuria, especially in the general population. Our objective was to answer these questions. We conducted a genomewide association study (GWAS) separately on two population-based cohorts, Ansung and Ansan, in the Korean Genome and Epidemiology Study (KoGES). The initial GWAS was carried out on the Ansung cohort, followed by a replication study on the Ansan cohort. A total of 5682 native Korean participants without a significant medical illness were classified into either control group (n = 3153) or prediabetic group (n = 2529). In the GWAS, we identified two susceptibility loci associated with prediabetes, one at 17p15.3-p15.1 in the GCK gene and another at 7p15.1 in YKT6. When variations in GCK and YKT6 were used as a model of prediabetes, this genetically determined prediabetes increased microalbuminuria. Multiple logistic regression analyses revealed that fasting glucose concentration in plasma and SNP rs2908289 in GCK were associated with microalbuminuria, and adjustment for age, gender, smoking history, systolic blood pressure, waist circumference, and serum triglyceride levels did not attenuate this association. Our results suggest that prediabetes and the associated SNPs may predispose to microalbuminuria before the diagnosis of diabetes mellitus. Further studies are needed to explore the details of the physiological and molecular mechanisms underlying this genetic association.

  10. Evidence for collective {delta}T{sub c} pinning in superconducting (K, Ba)BiO{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Harneit, W [Centre National de la Recherche Scientifique (CNRS), 38 -Grenoble (France). Lab. d` Etudes des Proprietes Electroniques des Solides; Klein, T [Centre National de la Recherche Scientifique (CNRS), 38 - Grenoble (France). Lab. d` Etudes des Proprietes Electroniques des Solides; Baril, L [Centre National de la Recherche Scientifique (CNRS), 38 - Grenoble (France). Lab. d` Etudes des Proprietes Electroniques des Solides; Escribe-Filippini, C [Centre National de la Recherche Scientifique (CNRS), 38 - Grenoble (France). Lab. d` Etudes des Proprietes Electroniques des Solides

    1996-10-10

    The nature of pinning has been investigated in the three-dimensional high-T{sub c} superconductor (K, Ba)BiO{sub 3}. We show that the magnetic-field dependence of the critical current deduced from pulsed-field magnetization measurements can be well described by the collective-pinning theory on a large temperature range 0.06sub c}<0.62. This permits us to construct a nonequilibrium H-T phase diagram including both the single-vortex and vortex bundle regimes. Furthermore, the temperature dependence of the collective-pinning length L{sub c} is in excellent agreement with a model of flux pinning induced by spatial fluctuations of the critical temperature ({delta}T{sub c} pinning model). (orig.).

  11. Structural Basis for Nucleotide Binding and Reaction Catalysis in Mevalonate Diphosphate Decarboxylase

    Energy Technology Data Exchange (ETDEWEB)

    Barta, Michael L.; McWhorter, William J.; Miziorko, Henry M.; Geisbrecht, Brian V. (UMKC)

    2012-09-17

    Mevalonate diphosphate decarboxylase (MDD) catalyzes the final step of the mevalonate pathway, the Mg{sup 2+}-ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP), producing isopentenyl diphosphate (IPP). Synthesis of IPP, an isoprenoid precursor molecule that is a critical intermediate in peptidoglycan and polyisoprenoid biosynthesis, is essential in Gram-positive bacteria (e.g., Staphylococcus, Streptococcus, and Enterococcus spp.), and thus the enzymes of the mevalonate pathway are ideal antimicrobial targets. MDD belongs to the GHMP superfamily of metabolite kinases that have been extensively studied for the past 50 years, yet the crystallization of GHMP kinase ternary complexes has proven to be difficult. To further our understanding of the catalytic mechanism of GHMP kinases with the purpose of developing broad spectrum antimicrobial agents that target the substrate and nucleotide binding sites, we report the crystal structures of wild-type and mutant (S192A and D283A) ternary complexes of Staphylococcus epidermidis MDD. Comparison of apo, MVAPP-bound, and ternary complex wild-type MDD provides structural information about the mode of substrate binding and the catalytic mechanism. Structural characterization of ternary complexes of catalytically deficient MDD S192A and D283A (k{sub cat} decreased 10{sup 3}- and 10{sup 5}-fold, respectively) provides insight into MDD function. The carboxylate side chain of invariant Asp{sup 283} functions as a catalytic base and is essential for the proper orientation of the MVAPP C3-hydroxyl group within the active site funnel. Several MDD amino acids within the conserved phosphate binding loop ('P-loop') provide key interactions, stabilizing the nucleotide triphosphoryl moiety. The crystal structures presented here provide a useful foundation for structure-based drug design.

  12. HIV-1 Promoter Single Nucleotide Polymorphisms Are Associated with Clinical Disease Severity.

    Directory of Open Access Journals (Sweden)

    Michael R Nonnemacher

    Full Text Available The large majority of human immunodeficiency virus type 1 (HIV-1 markers of disease progression/severity previously identified have been associated with alterations in host genetic and immune responses, with few studies focused on viral genetic markers correlate with changes in disease severity. This study presents a cross-sectional/longitudinal study of HIV-1 single nucleotide polymorphisms (SNPs contained within the viral promoter or long terminal repeat (LTR in patients within the Drexel Medicine CNS AIDS Research and Eradication Study (CARES Cohort. HIV-1 LTR SNPs were found to associate with the classical clinical disease parameters CD4+ T-cell count and log viral load. They were found in both defined and undefined transcription factor binding sites of the LTR. A novel SNP identified at position 108 in a known COUP (chicken ovalbumin upstream promoter/AP1 transcription factor binding site was significantly correlated with binding phenotypes that are potentially the underlying cause of the associated clinical outcome (increase in viral load and decrease in CD4+ T-cell count.

  13. Specific heat of ceramic and single crystal MgB{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Junod, A.; Wang, Y.; Bouquet, F.; Sheikin, I.; Toulemonde, P.; Eskildsen, M.R.; Eisterer, M.; Weber, H.W.; Lee, S.; Tajima, S

    2003-05-15

    The two-gap structure of MgB{sub 2} gives rise to unusual thermodynamic properties which depart markedly from the single-gap BCS model, both in their temperature- and field-dependence. We report measurements of the specific heat up to 16 T on ceramic and single crystal samples, which demonstrate these effects in bulk. The low-temperature mixed-state specific heat reveals a field-dependent anisotropy, and points to the existence of unusually large vortices, in agreement with local density-of-states measurements by scanning tunneling spectroscopy. It is finally shown that a suitable irradiation process nearly doubles H{sub c2} in the bulk.

  14. Synthesis, single-crystal structure refinement and Fe/T site preference in the ternary borides Fe {sub x}T{sub 7-x}B{sub 3} (T = Ru, Rh; 0 < x {<=} 1.5)

    Energy Technology Data Exchange (ETDEWEB)

    Fokwa, Boniface P.T. [Institut fuer Anorganische Chemie, Rheinisch-Westfaelische Technische Hochschule Aachen, D-52056 Aachen (Germany); Dronskowski, Richard [Institut fuer Anorganische Chemie, Rheinisch-Westfaelische Technische Hochschule Aachen, D-52056 Aachen (Germany)]. E-mail: drons@HAL9000.ac.rwth-aachen.de

    2007-01-31

    Single crystals of the borides Fe {sub x}Rh{sub 7-x}B{sub 3} (1 < x < 1.5) and Fe {sub x}Ru{sub 7-x}B{sub 3} (0 < x < 1) have been synthesized by arc-melting the elements in a water-cooled copper crucible under argon atmosphere. The silver-like products, structurally characterized by single-crystal X-ray analysis, adopt the hexagonal Th{sub 7}Fe{sub 3} structure type (space group P6{sub 3} mc, no. 186) with Z = 2. Their structures consist of layers of boron-centered trigonal prisms of rhodium or ruthenium (Rh;Ru) and iron on the one side, and one-dimensional channels of face-sharing octahedral (Rh;Ru){sub 6} clusters on the other. Unlike in FeRh{sub 6}B{sub 3}, the iron substitution takes place at two (6c and 2b) of the three available rhodium/ruthenium positions, with a preference for the 6c site in the case of the Fe {sub x}Rh{sub 7-x}B{sub 3} compounds but not for Fe {sub x}Ru{sub 7-x}B{sub 3}.

  15. Yb:Lu{sub 2}O{sub 3} hydrothermally-grown single-crystal and ceramic absorption spectra obtained between 298 and 80 K

    Energy Technology Data Exchange (ETDEWEB)

    Moore, Cheryl A. [Snake Creek Lasers LLC, 26741 State Route 267, Friendsville, PA 18818 (United States); Department of Chemistry and Center for Optical Materials Science and Engineering Technologies, Clemson University, Clemson, SC 29634-0973 (United States); Brown, David C., E-mail: dbrown@snakecreeklasers.com [Snake Creek Lasers LLC, 26741 State Route 267, Friendsville, PA 18818 (United States); Sanjeewa, Liurukara D.; McMillen, Colin D.; Kolis, Joseph W. [Department of Chemistry and Center for Optical Materials Science and Engineering Technologies, Clemson University, Clemson, SC 29634-0973 (United States)

    2016-06-15

    The hydrothermal growth, doping, and low temperature spectral characterization of Yb doped Lu{sub 2}O{sub 3} was investigated. The absorption of the lutetia-based sesquioxide laser material Yb:Lu{sub 2}O{sub 3} at temperatures of 80, 150, 200, 250, and 298 K, in the wavelength range of 850–1100 nm are reported. Data for both single crystal and ceramic Yb:Lu{sub 2}O{sub 3} were obtained. The resulting absorption cross-section data will enable the further evaluation of Yb:Lu{sub 2}O{sub 3} as a very promising high power cryogenic laser material.

  16. A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

    DEFF Research Database (Denmark)

    Pujolar, J.M.; Jacobsen, M.W.; Frydenberg, J.

    2013-01-01

    Reduced representation genome sequencing such as restriction-site-associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single-nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the Eu...... 425 loci and 376 918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome...

  17. Palindromic nucleotide analysis in human T cell receptor rearrangements.

    Directory of Open Access Journals (Sweden)

    Santosh K Srivastava

    Full Text Available Diversity of T cell receptor (TCR genes is primarily generated by nucleotide insertions upon rearrangement from their germ line-encoded V, D and J segments. Nucleotide insertions at V-D and D-J junctions are random, but some small subsets of these insertions are exceptional, in that one to three base pairs inversely repeat the sequence of the germline DNA. These short complementary palindromic sequences are called P nucleotides. We apply the ImmunoSeq deep-sequencing assay to the third complementarity determining region (CDR3 of the β chain of T cell receptors, and use the resulting data to study P nucleotides in the repertoire of naïve and memory CD8(+ and CD4(+ T cells. We estimate P nucleotide distributions in a cross section of healthy adults and different T cell subtypes. We show that P nucleotide frequency in all T cell subtypes ranges from 1% to 2%, and that the distribution is highly biased with respect to the coding end of the gene segment. Classification of observed palindromic sequences into P nucleotides using a maximum conditional probability model shows that single base P nucleotides are very rare in VDJ recombination; P nucleotides are primarily two bases long. To explore the role of P nucleotides in thymic selection, we compare P nucleotides in productive and non-productive sequences of CD8(+ naïve T cells. The naïve CD8(+ T cell clones with P nucleotides are more highly expanded.

  18. Growth and characterization of lead-free (K,Na)NbO{sub 3}-based piezoelectric single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hairui

    2016-10-19

    Lead-free piezoelectric materials have received increasing attention in the last decade, driven by environmental issues and health concerns. Of considerable interest is the (K,Na)NbO{sub 3} (KNN)-based system, which possesses a relatively high Curie temperature and good piezoelectric properties. Abundant publications on KNN-based polycrystalline ceramics increased the interest in studying their single-crystalline form, based on two major concerns. The first concern refers to the negative role of grain interactions on the electromechanical response. The second concern deals with domain engineering. The relationship between external electric field direction, crystallographic orientation, and spontaneous polarization vectors for a specific structure can be more readily established in single crystals and thus offers a pathway for an in-depth understanding of fundamental mechanism and potential applications. The exciting enhancement of both piezoelectric and ferroelectric response in lead-based single crystals also encourages the further exploration of KNN-based piezoelectric crystals, as they possess the same perovskite structure. The main goal of this thesis is to find possible approaches for improved electromechanical properties in KNN-based piezoelectric single crystals. In Chapter 2, the current development of KNN-based single crystals as piezoelectrics is reviewed, following a short introduction of fundamental knowledge on piezoelectrics and ferroelectrics. Both submerged-seed solution growth and top-seeded solution growth techniques were employed to produce single crystals, as described detailed in Chapter 3. Emphasis is subsequently placed on issues of the crystal growth process, effective methods to enhance electrical properties, and crystallographic orientation-dependent electrical properties in Li-, Ta-, and/or Sb-substituted KNN single crystals. The main conclusions from the crystal growth aspect are presented in Chapter 4 and can be summarized as follows

  19. Pulse shape discrimination properties of Gd{sub 3}Ga{sub 3}Al{sub 2}O{sub 12}:Ce,B single crystal in comparison with CsI:Tl

    Energy Technology Data Exchange (ETDEWEB)

    Rawat, S. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Department of Physics, Indian Institute of Technology, Roorkee 247667 (India); Tyagi, Mohit [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Netrakanti, P.K.; Kashyap, V.K.S.; Mitra, A. [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Singh, A.K.; Desai, D.G. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Kumar, G. Anil [Department of Physics, Indian Institute of Technology, Roorkee 247667 (India); Gadkari, S.C. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2016-12-21

    Single crystals of Gd{sub 3}Ga{sub 3}Al{sub 2}O{sub 12}:Ce,B and CsI:Tl were grown by Czochralski and Bridgman techniques, respectively. While both the crystals exhibited similar emission at about 550 nm, their scintillation decay times showed significantly different characteristics. The average scintillation decay time of Gd{sub 3}Ga{sub 3}Al{sub 2}O{sub 12}:Ce,B crystal was found to be about 284 ns for alpha excitation compared to 108 ns measured for a gamma source. On the other hand in CsI:Tl crystals, the alpha excitation resulted in a lower average decay time of 600 ns compared to 1200 ns with gamma excitation. Their pulse shape discrimination (PSD) for gamma and alpha radiations were studied by coupling the scintillators with photomultiplier tube or SiPM and employing an advanced digitizer as well as a conventional zero-crossing setup. In spite of having a poor α/γ light yield ratio, the PSD figure of merit and the difference of zero-crossing time in Gd{sub 3}Ga{sub 3}Al{sub 2}O{sub 12}:Ce,B crystals were found to be superior in comparison to CsI:Tl crystals.

  20. Separate Turbo Code and Single Turbo Code Adaptive OFDM Transmissions

    Directory of Open Access Journals (Sweden)

    Burr Alister

    2009-01-01

    Full Text Available Abstract This paper discusses the application of adaptive modulation and adaptive rate turbo coding to orthogonal frequency-division multiplexing (OFDM, to increase throughput on the time and frequency selective channel. The adaptive turbo code scheme is based on a subband adaptive method, and compares two adaptive systems: a conventional approach where a separate turbo code is used for each subband, and a single turbo code adaptive system which uses a single turbo code over all subbands. Five modulation schemes (BPSK, QPSK, 8AMPM, 16QAM, and 64QAM are employed and turbo code rates considered are and . The performances of both systems with high ( and low ( BER targets are compared. Simulation results for throughput and BER show that the single turbo code adaptive system provides a significant improvement.

  1. Error-free 5.1 Tbit/s data generation on a single-wavelength channel using a 1.28 Tbaud symbol rate

    DEFF Research Database (Denmark)

    Mulvad, Hans Christian Hansen; Galili, Michael; Oxenløwe, Leif Katsuo

    2009-01-01

    We demonstrate a record bit rate of 5.1 Tbit/s on a single wavelength using a 1.28 Tbaud OTDM symbol rate, DQPSK data-modulation, and polarisation-multiplexing. Error-free performance (BER......We demonstrate a record bit rate of 5.1 Tbit/s on a single wavelength using a 1.28 Tbaud OTDM symbol rate, DQPSK data-modulation, and polarisation-multiplexing. Error-free performance (BER...

  2. Lattice instability and soft phonons in single-crystal La/sub 2-//sub x/Sr/sub x/CuO4

    International Nuclear Information System (INIS)

    Boeni, P.; Axe, J.D.; Shirane, G.

    1988-01-01

    The dispersion of the low-lying phonon branches of several doped and undoped single crystals of La/sub 2-//sub x/Sr/sub x/CuO 4 have been investigated by using inelastic-neutron-scattering techniques. The zone-center modes are in good agreement with Raman measurements. The reported peaks in the phonon density of states show up at energies that correspond to extrema in the dispersion curves of the transverse and longitudinal acoustic branches near the zone boundary. The tetragonal-to-orthorhombic phase transition is caused by a softening of transverse-optic-phonon mode at the X point. The rotational nature of the soft mode leads to moderate weak electron-phonon coupling and the mode is unlikely to enhance significantly conventional phonon mediated superconductivity. We did not observe any evidence for the predicted breathing-mode instability near the zone boundary

  3. Relationship between single nucleotide polymorphism of glycogen synthase gene of Pacific oyster Crassostrea gigas and its glycogen content

    Science.gov (United States)

    Liu, Siwei; Li, Qi; Yu, Hong; Kong, Lingfeng

    2017-02-01

    Glycogen is important not only for the energy supplementary of oysters, but also for human consumption. High glycogen content can improve the stress survival of oyster. A key enzyme in glycogenesis is glycogen synthase that is encoded by glycogen synthase gene GYS. In this study, the relationship between single nucleotide polymorphisms (SNPs) in coding regions of Crassostrea gigas GYS (Cg-GYS) and individual glycogen content was investigated with 321 individuals from five full-sib families. Single-strand conformation polymorphism (SSCP) procedure was combined with sequencing to confirm individual SNP genotypes of Cg-GYS. Least-square analysis of variance was performed to assess the relationship of variation in glycogen content of C. gigas with single SNP genotype and SNP haplotype. As a consequence, six SNPs were found in coding regions to be significantly associated with glycogen content ( P glycogen content ( P glycogen content and provided molecular biological information for the selective breeding of good quality traits of C. gigas.

  4. BER analysis of DS-UWB system employing a laplace distribution model

    KAUST Repository

    Mehbodniya, Abolfazl; Aissa, Sonia; Adachi, Fumiyuki

    2011-01-01

    This letter takes a new approach to extract a closed-form expression for the bit error rate (BER) of direct-sequence ultra wideband (DS-UWB) system. In the analysis, the main signal is impaired by multi-user interference (MUI) and an external source

  5. A hierarchical nanostructure consisting of amorphous MnO{sub 2}, Mn{sub 3}O{sub 4} nanocrystallites, and single-crystalline MnOOH nanowires for supercapacitors

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Chi-Chang; Hung, Ching-Yun [Department of Chemical Engineering, National Tsing Hua University, Hsin-Chu 30013 (China); Chang, Kuo-Hsin [Department of Chemical Engineering, National Tsing Hua University, Hsin-Chu 30013 (China); Department of Chemical Engineering, National Chung Cheng University, Chia-Yi 621 (China); Yang, Yi-Lin [Department of Chemical Engineering, National Chung Cheng University, Chia-Yi 621 (China)

    2011-01-15

    In this communication, a porous hierarchical nanostructure consisting of amorphous MnO{sub 2} (a-MnO{sub 2}), Mn{sub 3}O{sub 4} nanocrystals, and single-crystalline MnOOH nanowires is designed for the supercapacitor application, which is prepared by a simple two-step electrochemical deposition process. Because of the gradual co-transformation of Mn{sub 3}O{sub 4} nanocrystals and a-MnO{sub 2} nanorods into an amorphous manganese oxide, the cycle stability of a-MnO{sub 2} is obviously enhanced by adding Mn{sub 3}O{sub 4}. This unique ternary oxide nanocomposite with 100-cycle CV activation exhibits excellent capacitive performances, i.e., excellent reversibility, high specific capacitances (470 F g{sup -1} in CaCl{sub 2}), high power property, and outstanding cycle stability. The highly porous microstructures of this composite before and after the 10,000-cycle CV test are examined by means of scanning electron microscopy (SEM) and transmission electron microscopy (TEM). (author)

  6. The nano-TiO{sub 2} exposure can induce hepatic inflammation involving in a JAK–STAT signalling pathway

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Jie [Soochow University, Department of Applied Biology, School of Basic Medical and Biological Sciences (China); Hong, Fashui, E-mail: hongfsh-cn@sina.com [Huaiyin Normal University, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection (China); Ze, Yuguan; Zhang, Yu-Qing, E-mail: sericult@suda.edu.cn [Soochow University, Department of Applied Biology, School of Basic Medical and Biological Sciences (China)

    2016-06-15

    TiO{sub 2} nanoparticles (TiO{sub 2} NPs) have unique physiochemical properties and thus are widely used in daily life. However, these nanoparticles also have potential toxic effects in humans and animals, and the issue of the security TiO{sub 2} NPs has also gained prominence. In this article, mice were administered a gavage instillation of 2.5, 5, or 10 mg/kg body weight TiO{sub 2} NPs (5–6 nm) for 90 days. We investigated whether TiO{sub 2} NPs activate the JAK–STAT signalling pathway, causing nano-TiO{sub 2}-induced hepatic toxicity. The results demonstrated that with increasing doses of TiO{sub 2} NPs the body weights of the mice body decreased, and the liver index, liver dysfunction, infiltration of inflammatory cells, and hepatocyte apoptosis and necrosis increased. Moreover, liver inflammation was accompanied by increased expression of Janus kinase 2, the signal transducers and activators of transcription 3, interleukin-6, cyclooxygenase-2, neutrophil gelatinase-associated lipocalin, purinergic receptor-7, and epithelial neutrophil-activating protein-78 and decreased expression of suppressors of cytokine signalling-1, peroxisome proliferator-activated receptor-γ, and peroxisome proliferator-activated receptor gamma coactivator-1 alpha. In summary, the activation of the JAK–STAT pathway may be involved in the hepatic inflammation induced by chronic nano-TiO{sub 2} toxicity.

  7. No association between a common single nucleotide polymorphism, rs4141463, in the MACROD2 gene and autism spectrum disorder.

    Science.gov (United States)

    Curran, Sarah; Bolton, Patrick; Rozsnyai, Kinga; Chiocchetti, Andreas; Klauck, Sabine M; Duketis, Eftichia; Poustka, Fritz; Schlitt, Sabine; Freitag, Christine M; Lee, Irene; Muglia, Pierandrea; Poot, Martin; Staal, Wouter; de Jonge, Maretha V; Ophoff, Roel A; Lewis, Cathryn; Skuse, David; Mandy, Will; Vassos, Evangelos; Fossdal, Ragnheidur; Magnusson, Páll; Hreidarsson, Stefan; Saemundsen, Evald; Stefansson, Hreinn; Stefansson, Kari; Collier, David

    2011-09-01

    The Autism Genome Project (AGP) Consortium recently reported genome-wide significant association between autism and an intronic single nucleotide polymorphism marker, rs4141463, within the MACROD2 gene. In the present study we attempted to replicate this finding using an independent case-control design of 1,170 cases with autism spectrum disorder (ASD) (874 of which fulfilled narrow criteria for Autism (A)) from five centers within Europe (UK, Germany, the Netherlands, Italy, and Iceland), and 35,307 controls. The combined sample size gave us a non-centrality parameter (NCP) of 11.9, with 93% power to detect allelic association of rs4141463 at an alpha of 0.05 with odds ratio of 0.84 (the best odds ratio estimate of the AGP Consortium data), and for the narrow diagnosis of autism, an NCP of 8.9 and power of 85%. Our case-control data were analyzed for association, stratified by each center, and the summary statistics were combined using the meta-analysis program, GWAMA. This resulted in an odds ratio (OR) of 1.03 (95% CI 0.944-1.133), with a P-value of 0.5 for ASD and OR of 0.99 (95% CI 0.88-1.11) with P-value = 0.85 for the Autism (A) sub-group. Therefore, this study does not provide support for the reported association between rs4141463 and autism. Copyright © 2011 Wiley-Liss, Inc.

  8. Thermodynamic and transport properties of single crystalline RCo{sub 2}Ge{sub 2} (R=Y, La–Nd, Sm–Tm)

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Tai, E-mail: taikong@iastate.edu [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Ames Laboratory, Iowa State University, Ames, IA 50011 (United States); Cunningham, Charles E. [Department of Physics, Grinnell College, Grinnell, IA 50112 (United States); Taufour, Valentin [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Bud' ko, Sergey L. [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Ames Laboratory, Iowa State University, Ames, IA 50011 (United States); Buffon, Malinda L.C. [Ames Laboratory, Iowa State University, Ames, IA 50011 (United States); Lin, Xiao [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Ames Laboratory, Iowa State University, Ames, IA 50011 (United States); Emmons, Heather [Department of Physics, Grinnell College, Grinnell, IA 50112 (United States); Canfield, Paul C., E-mail: canfield@ameslab.gov [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Ames Laboratory, Iowa State University, Ames, IA 50011 (United States)

    2014-05-01

    Single crystals of RCo{sub 2}Ge{sub 2} (R=Y, La–Nd, Sm–Tm) were grown using a self-flux method and were characterized by room-temperature powder X-ray diffraction; anisotropic, temperature and field dependent magnetization; temperature and field dependent, in-plane resistivity; and specific heat measurements. In this series, the majority of the moment-bearing members order antiferromagnetically; YCo{sub 2}Ge{sub 2} and LaCo{sub 2}Ge{sub 2} are non-moment-bearing. Ce is trivalent in CeCo{sub 2}Ge{sub 2} at high temperatures, and exhibits an enhanced electronic specific heat coefficient due to the Kondo effect at low temperatures. In addition, CeCo{sub 2}Ge{sub 2} shows two low-temperature anomalies in temperature-dependent magnetization and specific heat measurements. Three members (R=Tb–Ho) have multiple phase transitions above 1.8 K. Eu appears to be divalent with total angular momentum L=0. Both EuCo{sub 2}Ge{sub 2} and GdCo{sub 2}Ge{sub 2} manifest essentially isotropic paramagnetic properties consistent with J=S=7/2. Clear magnetic anisotropy for rare-earth members with finite L was observed, with ErCo{sub 2}Ge{sub 2} and TmCo{sub 2}Ge{sub 2} manifesting planar anisotropy and the rest members manifesting axial anisotropy. The experimentally estimated crystal electric field (CEF) parameters B{sub 2}{sup 0} were calculated from the anisotropic paramagnetic θ{sub ab} and θ{sub c} values and follow a trend that agrees well with theoretical predictions. The ordering temperatures, T{sub N}, as well as the polycrystalline averaged paramagnetic Curie–Weiss temperature, Θ{sub avg}, for the heavy rare-earth members deviate from the de Gennes scaling, as the magnitude of both is the highest for Tb, which is sometimes seen for extremely axial systems. Except for SmCo{sub 2}Ge{sub 2}, metamagnetic transitions were observed at 1.8 K for all members that ordered antiferromagnetically. - Highlights: • Single crystalline RCo{sub 2}Ge{sub 2} (R=Y, La–Nd, Sm

  9. Spontaneous preterm birth and single nucleotide gene polymorphisms: a recent update.

    Science.gov (United States)

    Sheikh, Ishfaq A; Ahmad, Ejaz; Jamal, Mohammad S; Rehan, Mohd; Assidi, Mourad; Tayubi, Iftikhar A; AlBasri, Samera F; Bajouh, Osama S; Turki, Rola F; Abuzenadah, Adel M; Damanhouri, Ghazi A; Beg, Mohd A; Al-Qahtani, Mohammed

    2016-10-17

    Preterm birth (PTB), birth at PTBs are spontaneous with about a half without any apparent cause and the other half associated with a number of risk factors. Genetic factors are one of the significant risks for PTB. The focus of this review is on single nucleotide gene polymorphisms (SNPs) that are reported to be associated with PTB. A comprehensive evaluation of studies on SNPs known to confer potential risk of PTB was done by performing a targeted PubMed search for the years 2007-2015 and systematically reviewing all relevant studies. Evaluation of 92 studies identified 119 candidate genes with SNPs that had potential association with PTB. The genes were associated with functions of a wide spectrum of tissue and cell types such as endocrine, tissue remodeling, vascular, metabolic, and immune and inflammatory systems. A number of potential functional candidate gene variants have been reported that predispose women for PTB. Understanding the complex genomic landscape of PTB needs high-throughput genome sequencing methods such as whole-exome sequencing and whole-genome sequencing approaches that will significantly enhance the understanding of PTB. Identification of high risk women, avoidance of possible risk factors, and provision of personalized health care are important to manage PTB.

  10. regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution.

    Science.gov (United States)

    Zhang, Xinjun; Li, Meng; Lin, Hai; Rao, Xi; Feng, Weixing; Yang, Yuedong; Mort, Matthew; Cooper, David N; Wang, Yue; Wang, Yadong; Wells, Clark; Zhou, Yaoqi; Liu, Yunlong

    2017-09-01

    While synonymous single-nucleotide variants (sSNVs) have largely been unstudied, since they do not alter protein sequence, mounting evidence suggests that they may affect RNA conformation, splicing, and the stability of nascent-mRNAs to promote various diseases. Accurately prioritizing deleterious sSNVs from a pool of neutral ones can significantly improve our ability of selecting functional genetic variants identified from various genome-sequencing projects, and, therefore, advance our understanding of disease etiology. In this study, we develop a computational algorithm to prioritize sSNVs based on their impact on mRNA splicing and protein function. In addition to genomic features that potentially affect splicing regulation, our proposed algorithm also includes dozens structural features that characterize the functions of alternatively spliced exons on protein function. Our systematical evaluation on thousands of sSNVs suggests that several structural features, including intrinsic disorder protein scores, solvent accessible surface areas, protein secondary structures, and known and predicted protein family domains, show significant differences between disease-causing and neutral sSNVs. Our result suggests that the protein structure features offer an added dimension of information while distinguishing disease-causing and neutral synonymous variants. The inclusion of structural features increases the predictive accuracy for functional sSNV prioritization.

  11. The spectroscopy investigation of ZnWO{sub 4}:Tm{sup 3+} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Yang Fugui, E-mail: ruopiao@fjirsm.ac.cn [Department of Electronic Information Science, Fujian Jiangxia University, Fuzhou, Fujian 350108 (China); Tu Chaoyang [Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002 (China)

    2012-09-15

    Highlights: Black-Right-Pointing-Pointer The spectroscopy and refractive index of single crystal ZnWO{sub 4}:Tm{sup 3+} are investigated systematically. Black-Right-Pointing-Pointer The Judd-Ofelt parameters are obtained. Black-Right-Pointing-Pointer The gain cross sections at {approx}2 {mu}m are estimated by reciprocity method (RM). Black-Right-Pointing-Pointer The laser operation at {approx}2 {mu}m is discussed. - Abstract: The single crystal ZnWO{sub 4}:Tm{sup 3+} has been grown by Czochralski method. The XRD, refractive index, absorption and fluorescence spectra are measured. The Judd-Ofelt parameters{Omega}{sub 2}, {Omega}{sub 4}, {Omega}{sub 6} are obtained to be 6.3 Multiplication-Sign 10{sup -20}, 1.3 Multiplication-Sign 10{sup -20}, 1.4 Multiplication-Sign 10{sup -20} cm{sup 2}, respectively. The fluorescence decay time of the {sup 3}H{sub 4} level is measured to be 0.113 ms and the quantum efficiency is 57%. The gain cross sections corresponding to {sup 3}F{sub 4}{yields}{sup 3}H{sub 6} transition at {approx}2 {mu}m are estimated by the reciprocity method (RM). The strong gain at {approx}2 {mu}m indicates that the ZnWO{sub 4}:Tm{sup 3+} crystal is a promising laser host for {approx}2 {mu}m laser.

  12. Single-step synthesis of In{sub 2}O{sub 3} nanowires decorated with TeO{sub 2} nanobeads and their acetone-sensing properties

    Energy Technology Data Exchange (ETDEWEB)

    Park, Sunghoon; Kheel, Hyejoon; Sun, Gun-Joo; Lee, Chongmu [Inha University, Department of Materials Science and Engineering, Incheon (Korea, Republic of); Park, Sang Eon [Inha University, Department of Chemistry, Incheon (Korea, Republic of)

    2016-04-15

    In{sub 2}O{sub 3} nanowires decorated with TeO{sub 2} nanobeads were synthesized by a facile single-step thermal evaporation process, and their acetone-gas-sensing properties were examined. The diameters and lengths of the In{sub 2}O{sub 3} nanowires ranged from 10 to 20 nm and up to 100 μm, respectively, whereas the diameters of the TeO{sub 2} beads ranged from 50 to 200 nm. The TeO{sub 2}-decorated In{sub 2}O{sub 3} nanowire sensor showed stronger response to acetone gas than the pristine In{sub 2}O{sub 3} nanowire sensor. The pristine and TeO{sub 2}-decorated In{sub 2}O{sub 3} nanowires exhibited sensitivity of ∝10.13 and ∝24.87, respectively, to 200 ppm acetone at 300 C. The decorated nanowire sensor also showed much more rapid response and recovery than the latter. Both sensors showed the strongest response to acetone gas at 300 C, respectively. The mechanism and origin of the enhanced acetone-gas-sensing performance of the TeO{sub 2}-decorated In{sub 2}O{sub 3} nanowire sensor compared to the pristine In{sub 2}O{sub 3} nanowire sensor were discussed in detail. The enhanced sensing performance of the TeO{sub 2}-decorated In{sub 2}O{sub 3} nanowire is mainly due to the modulation of the potential barrier height at the TeO{sub 2}-In{sub 2}O{sub 3} interface, high catalytic activity of TeO{sub 2,} and creation of active adsorption sites by incorporation of TeO{sub 2}. (orig.)

  13. Structural phase transitions in Bi[sub 2]V[sub 1[minus]x]Ge[sub x]O[sub 5. 5[minus]x/2] (x = 0. 2, 0. 4, and 0. 6) single crystals: X-ray crystallographic study

    Energy Technology Data Exchange (ETDEWEB)

    Sooryanarayana, K.; Guru Row, T.N.; Varma, K.B.R. (Indian Inst. of Science, Bangalore (India))

    1999-02-01

    Single crystals of Bi[sub 2]V[sub 1[minus]x]Ge[sub x]O[sub 5.5[minus]x/2] (x = 0.2, 0.4, and 0.6) were grown by slow cooling of melts. Bismuth vanadate transforms from an orthorhombic to a tetragonal structure and subsequently to an orthorhombic system when the Ge[sup 4+] concentration was varied from x = 0.2 to x = 0.6. All of these compositions crystallized in polar space groups (Aba2, F4mm, and Fmm2 for x = 0.2, 0.4, and 0.6, respectively). The structures were fully determined by single crystal X-ray diffraction studies.

  14. Single nucleotide polymorphisms of ADH1B, ADH1C and ALDH2 genes and esophageal cancer: A population-based case-control study in China

    NARCIS (Netherlands)

    Wu, M.; Chang, S.; Kampman, E.; Kok, F.J.

    2013-01-01

    Alcohol drinking is a major risk factor for esophageal cancer (EC) and the metabolism of ethanol has been suggested to play an important role in esophageal carcinogenesis. Epidemiologic studies, including genomewide association studies (GWAS), have identified single nucleotide polymorphisms (SNPs)

  15. Organized single-molecule magnets: direct observation of new Mn{sub 12} derivatives on gold

    Energy Technology Data Exchange (ETDEWEB)

    Cornia, A.; Fabretti, A.C.; Pacchioni, M.; Zobbi, L. E-mail: lzobbi@unimo.it; Bonacchi, D.; Caneschi, A.; Gatteschi, D.; Biagi, R.; Del Pennino, U.; De Renzi, V.; Gurevich, L.; Zant, H.S.J. van der

    2004-05-01

    Gold adsorbates of the dodecamanganese(III,IV) single-molecule magnet (SMM) [Mn{sub 12}O{sub 12}(L){sub 16}(H{sub 2}O){sub 4}] where L=16-(acetylthio)hexadecanoate have been prepared and investigated by X-ray photoelectron spectroscopy and scanning tunneling microscopy (STM). The successful imaging of Mn{sub 12} molecules by STM represents a first step toward the magnetic addressing of individual SMMs and the development of molecule-based devices for magnetic information storage.

  16. BER IMPROVEMENT OF WIRELESS LAN IEEE 802.11 STANDARD USING WAVELET PACKET TRANSFORMS

    Directory of Open Access Journals (Sweden)

    Sanjeev Kumar

    2012-09-01

    Full Text Available High data rates and spectral efficiency is the main requirements for wireless communication systems. Orthogonal Frequency Division Multiplexing (OFDM is a special form of multi carrier transmission used to achieve high data rates of the various WLAN standards. WLAN uses an Inverse Fast Fourier Transform (IFFT at the transmitter to modulate a high bit-rate signal onto a number of carriers and ensure orthogonality between the carriers. The FFT-OFDM has a disadvantage that it is inherently inflexible and requires a complex IFFT core. Recently, Wavelet Packet Transform is proposed as an alternate to FFT. It is a multiplexing method in which data is assigned to wavelet sub bands having different time and frequency resolutions. This paper presents a BER analysis of Fourier-based OFDM (FFT-OFDM and Wavelet Packet based OFDM (WPT-OFDM in WLAN standard (IEEE 802.11a. The performance of FFT and WPT OFDM for various modulation techniques such as PSK, DPSK and QAM for varying values of M was evaluated in AWGN Channel.

  17. Association of prediabetes-associated single nucleotide polymorphisms with microalbuminuria

    Science.gov (United States)

    Choi, Jong Wook; Moon, Shinje; Jang, Eun Jung; Lee, Chang Hwa; Park, Joon-Sung

    2017-01-01

    Increased glycemic exposure, even below the diagnostic criteria for diabetes mellitus, is crucial in the pathogenesis of diabetic microvascular complications represented by microalbuminuria. Nonetheless, there is limited evidence regarding which single nucleotide polymorphisms (SNPs) are associated with prediabetes and whether genetic predisposition to prediabetes is related to microalbuminuria, especially in the general population. Our objective was to answer these questions. We conducted a genomewide association study (GWAS) separately on two population-based cohorts, Ansung and Ansan, in the Korean Genome and Epidemiology Study (KoGES). The initial GWAS was carried out on the Ansung cohort, followed by a replication study on the Ansan cohort. A total of 5682 native Korean participants without a significant medical illness were classified into either control group (n = 3153) or prediabetic group (n = 2529). In the GWAS, we identified two susceptibility loci associated with prediabetes, one at 17p15.3-p15.1 in the GCK gene and another at 7p15.1 in YKT6. When variations in GCK and YKT6 were used as a model of prediabetes, this genetically determined prediabetes increased microalbuminuria. Multiple logistic regression analyses revealed that fasting glucose concentration in plasma and SNP rs2908289 in GCK were associated with microalbuminuria, and adjustment for age, gender, smoking history, systolic blood pressure, waist circumference, and serum triglyceride levels did not attenuate this association. Our results suggest that prediabetes and the associated SNPs may predispose to microalbuminuria before the diagnosis of diabetes mellitus. Further studies are needed to explore the details of the physiological and molecular mechanisms underlying this genetic association. PMID:28158221

  18. Effect of Post-Harvest Treatments on Enzyme Activity and Quality of Cold Stored Ber Fruit

    Directory of Open Access Journals (Sweden)

    Sukhjit K. JAWANDHA

    2012-11-01

    Full Text Available Ber (Zizyphus mauritiana Lamk fruits are perishable in nature and have poor shelf- life. To extend the storage life of ber fruits different post-harvest treatments, like CaCl2 (0.5, 1.0 and 2.0%, Ca(NO32 (0.5, 1.0 and 2.0%, gibberellic acid (GA3 (20, 40 and 60 ppm and Bavistin (0.1% were given to fruits and their effect was studied on the storage life and quality of Umran ber (Zizyphus mauritiana Lamk fruits under cold storage conditions. Fruits of uniform size and colour were harvested, from healthy plants, and subjected to post harvest dip of different chemicals, before packing in CFB boxes and placed in cold storage (3-5C and 85-90% RH They have been evaluated after 10, 20 and 30 days of storage for physiological loss in weight (PLW, firmness, pectin methyl esterase (PME activity and palatability rating. The PLW increased and fruit firmness decreased during storage at each treatment. The sensory rating increased up to 10 days at all treatments, except control but subsequently it decreased during storage. The increase rate in PME activity was faster, up to 10 days, in untreated fruits, while treated fruits showed slower rise in PME activity, up to 20 days with a decline afterwards. It can be concluded that ber fruits can be stored up to 20 days by post-harvest treatment using GA3 at 60 ppm, with acceptable quality.

  19. Effect of Post-Harvest Treatments on Enzyme Activity and Quality of Cold Stored Ber Fruit

    Directory of Open Access Journals (Sweden)

    Sukhjit K. JAWANDHA

    2012-11-01

    Full Text Available Ber (Zizyphus mauritiana Lamk fruits are perishable in nature and have poor shelf- life. To extend the storage life of ber fruits different post-harvest treatments, like CaCl2 (0.5, 1.0 and 2.0%, Ca(NO32 (0.5, 1.0 and 2.0%, gibberellic acid (GA3 (20, 40 and 60 ppm and Bavistin (0.1% were given to fruits and their effect was studied on the storage life and quality of �Umran� ber (Zizyphus mauritiana Lamk fruits under cold storage conditions. Fruits of uniform size and colour were harvested, from healthy plants, and subjected to post harvest dip of different chemicals, before packing in CFB boxes and placed in cold storage (3-5�C and 85-90% RH They have been evaluated after 10, 20 and 30 days of storage for physiological loss in weight (PLW, firmness, pectin methyl esterase (PME activity and palatability rating. The PLW increased and fruit firmness decreased during storage at each treatment. The sensory rating increased up to 10 days at all treatments, except control but subsequently it decreased during storage. The increase rate in PME activity was faster, up to 10 days, in untreated fruits, while treated fruits showed slower rise in PME activity, up to 20 days with a decline afterwards. It can be concluded that ber fruits can be stored up to 20 days by post-harvest treatment using GA3 at 60 ppm, with acceptable quality.

  20. BER Reduction for mQAM High-Speed Tranmission in Optical Fiber ...

    African Journals Online (AJOL)

    The study was conducted in a software cosimulation environment with VPITransmissionMaker and Matlab software. The simulation results showed that error correcting codes and particularly LDPC codes are effective and provide satisfactory solutions to reduce the BER by fighting against optical transmission channel ...

  1. The effects of noncoding aquaporin-4 single-nucleotide polymorphisms on cognition and functional progression of Alzheimer's disease.

    Science.gov (United States)

    Burfeind, Kevin G; Murchison, Charles F; Westaway, Shawn K; Simon, Matthew J; Erten-Lyons, Deniz; Kaye, Jeffrey A; Quinn, Joseph F; Iliff, Jeffrey J

    2017-09-01

    The glymphatic system is a brain-wide perivascular network that facilitates clearance of proteins, including amyloid β, from the brain interstitium through the perivascular exchange of cerebrospinal fluid and interstitial fluid. The astrocytic water channel aquaporin-4 (AQP4) is required for glymphatic system function, and impairment of glymphatic function in the aging brain is associated with altered AQP4 expression and localization. In human cortical tissue, alterations in AQP4 expression and localization are associated with Alzheimer's disease (AD) status and pathology. Although this suggests a potential role for AQP4 in the development or progression of AD, the relationship between of naturally occurring variants in the human AQP4 gene and cognitive function has not yet been evaluated. Using data from several longitudinal aging cohorts, we investigated the association between five AQP4 single-nucleotide polymorphisms (SNPs) and the rate of cognitive decline in participants with a diagnosis of AD. None of the five SNPs were associated with different rates of AD diagnosis, age of dementia onset in trial subjects. No association between AQP4 SNPs with histological measures of AD pathology, including Braak stage or neuritic plaque density was observed. However, AQP4 SNPs were associated with altered rates of cognitive decline after AD diagnosis, with two SNPS (rs9951307 and rs3875089) associated with slower cognitive decline and two (rs3763040 and rs3763043) associated with more rapid cognitive decline after AD diagnosis. These results provide the first evidence that variations in the AQP4 gene, whose gene product AQP4 is vital for glymphatic pathway function, may modulate the progression of cognitive decline in AD.

  2. Development of electrolyte-supported intermediate-temperature single-chamber solid oxide fuel cells using Ln{sub 0.7}Sr{sub 0.3}Fe{sub 0.8}Co{sub 0.2}O{sub 3-{delta}} (Ln = Pr, La, Gd) cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz de Larramendi, I.; Ruiz de Larramendi, J.I.; Rojo, T. [Departamento de Quimica Inorganica, Universidad del Pais Vasco, Apdo.644, 48080 Bilbao (Spain); Lamas, D.G.; Cabezas, M.D.; Walsoee de Reca, N.E. [CINSO, CONICET-CITEFA, J.B. de La Salle 4397 (B1603ALO) Villa Martelli, Pcia. de Buenos Aires (Argentina)

    2009-09-05

    Iron-cobalt-based perovskite oxides with general formula Ln{sub 0.7}Sr{sub 0.3}Fe{sub 0.8}Co{sub 0.2}O{sub 3-{delta}} (where Ln = La, Pr and Gd) have been investigated for their application as intermediate-temperature cathodes in solid oxide fuel cells (SOFCs). Powdered samples of these materials were synthesized by a novel gel combustion process and then characterized by X-ray powder diffraction (XPD) and scanning electron microscopy (SEM). XPD patterns were satisfactorily indexed with an orthorhombic GdFeO{sub 3}-type structure and, for all samples, a mean particle size of less than 1 {mu}m was estimated from the SEM data. Experimental single-chamber SOFCs using with these materials as cathodes and NiO-SDC (samaria-doped ceria) and SDC as anode and electrolyte, respectively, were evaluated at 600 C in a methane/oxygen mixtures. Peak power densities of 65.4, 48.7 and 46.2 mW cm{sup -2} were obtained for Ag vertical stroke Ln{sub 0.7}Sr{sub 0.3}Fe{sub 0.8}Co{sub 0.2}O{sub 3-{delta}} vertical stroke SDC vertical stroke NiO-SDC vertical stroke Pt cells with Ln = Pr, La and Gd, respectively. The relatively high power density obtained for the Pr compound shows that it could be an interesting material for cathode of single-chamber SOFCs. (author)

  3. Effects of junction resistance and counterelectrode material on point-contact tunneling into single- and polycrystalline YBa/sub 2/Cu/sub 3/O/sub 7-y/

    Energy Technology Data Exchange (ETDEWEB)

    Moog, E.R.; Hawley, M.E.; Gray, K.E.; Liu, J.Z.; Hinks, D.G.; Capone, D.W. II; Downey, J.

    1988-06-01

    The effects of junction resistance and counterelectrode material on the results of point-contact tunneling studies into single- and polycrystalline YBa/sub 2/Cu/sub 3/O/sub 7-y/ are illustrated. Although reasonably symmetric I(V) curves predominantly indicate energy gap values /Delta/ /approx/ 20 meV, large asymmetries are often found for high-resistance junctions. Very low-resistance junctions show the expected behavior of pure metallic bridge and indicate /Delta/ /approx/ 25-30 meV.

  4. The Q705K and F359L Single-Nucleotide Polymorphisms of NOD-Like Receptor Signaling Pathway: Association with Chronic Pancreatitis, Pancreatic Cancer, and Periodontitis.

    Science.gov (United States)

    Miskiewicz, Andrzej; Szparecki, Grzegorz; Durlik, Marek; Rydzewska, Grażyna; Ziobrowski, Ireneusz; Górska, Renata

    2015-12-01

    The aim of this study was to establish the correlation between the occurrence of Q705K and F359L polymorphisms in patients diagnosed with pancreatic diseases and periodontal conditions of various degrees of severity. The above-mentioned genetic markers were assessed in patients with pancreatic cancer (n = 18) and chronic pancreatitis (n = 39) as well as in a healthy control group (n = 115). The established inclusion criteria were the following: Caucasian descent, non-smoking, and age range 20-80, with different levels of periodontitis activity according to S. Offenbacher's scale. The genotyping reactions were performed by means of an RT-PCR with the use of TaqMan(®) genotyping assay. Results of the study revealed that the state of periodontium was significantly worse in patients with chronic pancreatitis. The Q705K and F359L polymorphisms were associated with more advanced cases of periodontitis measured by clinical attachment level, whereas the Q705K was associated with intensified bleeding index. Furthermore, the F359L single-nucleotide polymorphism was significantly higher in the group with chronic pancreatitis (p periodontitis, pancreatic cancer, and chronic pancreatitis. These findings might constitute the basis for a new diagnostic and therapeutic approach.

  5. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms.

    Science.gov (United States)

    Taillon-Miller, P; Gu, Z; Li, Q; Hillier, L; Kwok, P Y

    1998-07-01

    An efficient strategy to develop a dense set of single-nucleotide polymorphism (SNP) markers is to take advantage of the human genome sequencing effort currently under way. Our approach is based on the fact that bacterial artificial chromosomes (BACs) and P1-based artificial chromosomes (PACs) used in long-range sequencing projects come from diploid libraries. If the overlapping clones sequenced are from different lineages, one is comparing the sequences from 2 homologous chromosomes in the overlapping region. We have analyzed in detail every SNP identified while sequencing three sets of overlapping clones found on chromosome 5p15.2, 7q21-7q22, and 13q12-13q13. In the 200.6 kb of DNA sequence analyzed in these overlaps, 153 SNPs were identified. Computer analysis for repetitive elements and suitability for STS development yielded 44 STSs containing 68 SNPs for further study. All 68 SNPs were confirmed to be present in at least one of the three (Caucasian, African-American, Hispanic) populations studied. Furthermore, 42 of the SNPs tested (62%) were informative in at least one population, 32 (47%) were informative in two or more populations, and 23 (34%) were informative in all three populations. These results clearly indicate that developing SNP markers from overlapping genomic sequence is highly efficient and cost effective, requiring only the two simple steps of developing STSs around the known SNPs and characterizing them in the appropriate populations.

  6. Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice.

    Science.gov (United States)

    Sharma, Niharika; Dang, Trang Minh; Singh, Namrata; Ruzicic, Slobodan; Mueller-Roeber, Bernd; Baumann, Ute; Heuer, Sigrid

    2018-01-08

    Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown. Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which

  7. KeyPathwayMiner 4.0

    DEFF Research Database (Denmark)

    Alcaraz, Nicolas; Pauling, Josch; Batra, Richa

    2014-01-01

    release of KeyPathwayMiner (version 4.0) that is not limited to analyses of single omics data sets, e.g. gene expression, but is able to directly combine several different omics data types. Version 4.0 can further integrate existing knowledge by adding a search bias towards sub-networks that contain...... (avoid) genes provided in a positive (negative) list. Finally the new release now also provides a set of novel visualization features and has been implemented as an app for the standard bioinformatics network analysis tool: Cytoscape. CONCLUSION: With KeyPathwayMiner 4.0, we publish a Cytoscape app...

  8. Single nucleotide polymorphisms of one-carbon metabolism and cancers of the esophagus, stomach, and liver in a Chinese population.

    Directory of Open Access Journals (Sweden)

    Shen-Chih Chang

    Full Text Available One-carbon metabolism (folate metabolism is considered important in carcinogenesis because of its involvement in DNA synthesis and biological methylation reactions. We investigated the associations of single nucleotide polymorphisms (SNPs in folate metabolic pathway and the risk of three GI cancers in a population-based case-control study in Taixing City, China, with 218 esophageal cancer cases, 206 stomach cancer cases, 204 liver cancer cases, and 415 healthy population controls. Study participants were interviewed with a standardized questionnaire, and blood samples were collected after the interviews. We genotyped SNPs of the MTHFR, MTR, MTRR, DNMT1, and ALDH2 genes, using PCR-RFLP, SNPlex, or TaqMan assays. To account for multiple comparisons and reduce the chances of false reports, we employed semi-Bayes (SB shrinkage analysis. After shrinkage and adjusting for potential confounding factors, we found positive associations between MTHFR rs1801133 and stomach cancer (any T versus C/C, SB odds-ratio [SBOR]: 1.79, 95% posterior limits: 1.18, 2.71 and liver cancer (SBOR: 1.51, 95% posterior limits: 0.98, 2.32. There was an inverse association between DNMT1 rs2228612 and esophageal cancer (any G versus A/A, SBOR: 0.60, 95% posterior limits: 0.39, 0.94. In addition, we detected potential heterogeneity across alcohol drinking status for ORs relating MTRR rs1801394 to esophageal (posterior homogeneity P = 0.005 and stomach cancer (posterior homogeneity P = 0.004, and ORs relating MTR rs1805087 to liver cancer (posterior homogeneity P = 0.021. Among non-alcohol drinkers, the variant allele (allele G of these two SNPs was inversely associated with the risk of these cancers; while a positive association was observed among ever-alcohol drinkers. Our results suggest that genetic polymorphisms related to one-carbon metabolism may be associated with cancers of the esophagus, stomach, and liver. Heterogeneity across alcohol consumption status of

  9. Regulation of nucleotide excision repair through ubiquitination

    Institute of Scientific and Technical Information of China (English)

    Jia Li; Audesh Bhat; Wei Xiao

    2011-01-01

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

  10. Crystallization of Zr<sub>2sub>PdxCu>1-xsub> and Zr<sub>2sub>NixCu>1-xsub> Metallic Glass

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Min [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    One interesting aspect of rretallic glasses is the numerous instances of the deviation of the phase selection from the amorphous state to thermodynamically stable phases during the crystallization process. Their devitrification pathways allow us to study the relationship between the original amorphous structure and their crystalline counter parts. Among the various factors of phase selections, size and electronic effects have been most extensively studied. Elucidating the phase selection process of a glassy alloy will be helpful to fill in the puzzle of the changes from disordered to ordered structures. In this thesis, Two model Zr<sub>2sub>PdxCu>1-xsub> and Zr<sub>2sub>NixCu>1-xsub> (x = 0, 0.25, 0.5, 0.75 and 1) glassy systems were investigated since: (1) All of the samples can be made into a homogenous metallic glass; (2) The atomic radii differ from Pd to Cu is by 11%, while Ni has nearly the identical atomic size compare to Cu. Moreover, Pd and Ni differ by only one valence electron from Cu. Thus, these systems are ideal to test the idea of the effects of electronic structure and size factors; (3) The small number of components in these pseudo binary systems readily lend themselves to theoretical modeling. Using high temperature X-ray diffraction (HTXRD) and thermal analysis, topological, size, electronic, bond and chemical distribution factors on crystallization selections in Zr<sub>2sub>PdxCu>1-xsub> and Zr<sub>2sub>NixCu>1-xsub> metallic glass have been explored. All Zr<sub>2sub>PdxCu>1-xsub> compositions share the same Cu11b phase with different pathways of meta-stable, icosahedral quasicrystalline phase (i-phase), and C16 phase formations. The quasicrystal phase formation is topologically related to the increasing icosahedral short range order (SRO) with Pd content in Zr<sub>2sub>PdxCu>1-xsub> system. Meta-stable C16 phase is competitive with

  11. Untersuchungen über Veronica triloba (Opiz) Kerner in Rheinhessen

    OpenAIRE

    Oesau, Albert

    1981-01-01

    Untersuchungen in den Jahren 1977-1979 ergaben, daß Veronica triloba (Opiz) Kerner, eine Sippe aus dem Veronica hederifolia-Aggregat, in Rheinhessen überraschenderweise weit verbreitet ist und bisher übersehen wurde. Sie siedelt vor allem in Ackerunkraut- und Felsgrus-Gesellschaften sowie lückigen Trockenrasen, ohne eine gesellschaftsspezifische Bindung zu zeigen. Gut ausgeprägte morphologische Merkmale gestatten eine sichere Differenzierung gegenüber den übrigen Sippenvertretern V. hederifol...

  12. Analysis of different sub-carrier allocation of M-ary QAM-OFDM downlink in RoF system

    Science.gov (United States)

    Shao, Yu-feng; Chen, Luo; Wang, An-rong; Zhao, Yun-jie; Long, Ying; Ji, Xing-ping

    2018-01-01

    In this paper, the performance of a 60 GHz radio over fiber (RoF) system with 4/16/64 quadrature amplitude modulation (QAM) orthogonal frequency division multiplexing (OFDM) downstream signals is studied. Delivery of 10 Gbit/s M-ary QAM (MQAM) OFDM signals through the 20-km-long single-mode fiber (SMF) is complicated in terms of intensity modulation and direct detection (IM/DD). Using self-homodyne method, the beating of two independent light waves generating the millimeter-wave at the photodetector can be down-converted to baseband in the electrical domain. Meanwhile, three kinds of sub-carrier arrangement schemes are compared and discussed, and the simulation results show that lower peak-to-average power ratio ( PAPR) can be obtained adopting the adjacent scheme. At bit error rate ( BER) of 10-3, the receiver sensitivity using 4QAM-OFDM sub-carrier signal is almost enhanced by 4 dB and 9 dB compared with those of 16QAM-OFDM signal and 64QAM-OFDM signal.

  13. Polymorphisms in inflammation pathway genes and endometrial cancer risk

    Science.gov (United States)

    Delahanty, Ryan J.; Xiang, Yong-Bing; Spurdle, Amanda; Beeghly-Fadiel, Alicia; Long, Jirong; Thompson, Deborah; Tomlinson, Ian; Yu, Herbert; Lambrechts, Diether; Dörk, Thilo; Goodman, Marc T.; Zheng, Ying; Salvesen, Helga B.; Bao, Ping-Ping; Amant, Frederic; Beckmann, Matthias W.; Coenegrachts, Lieve; Coosemans, An; Dubrowinskaja, Natalia; Dunning, Alison; Runnebaum, Ingo B.; Easton, Douglas; Ekici, Arif B.; Fasching, Peter A.; Halle, Mari K.; Hein, Alexander; Howarth, Kimberly; Gorman, Maggie; Kaydarova, Dylyara; Krakstad, Camilla; Lose, Felicity; Lu, Lingeng; Lurie, Galina; O’Mara, Tracy; Matsuno, Rayna K.; Pharoah, Paul; Risch, Harvey; Corssen, Madeleine; Trovik, Jone; Turmanov, Nurzhan; Wen, Wanqing; Lu, Wei; Cai, Qiuyin; Zheng, Wei; Shu, Xiao-Ou

    2013-01-01

    Background Experimental and epidemiological evidence have suggested that chronic inflammation may play a critical role in endometrial carcinogenesis. Methods To investigate this hypothesis, a two-stage study was carried out to evaluate single nucleotide polymorphisms (SNPs) in inflammatory pathway genes in association with endometrial cancer risk. In stage 1, 64 candidate pathway genes were identified and 4,542 directly genotyped or imputed SNPs were analyzed among 832 endometrial cancer cases and 2,049 controls, using data from the Shanghai Endometrial Cancer Genetics Study. Linkage disequilibrium of stage 1 SNPs significantly associated with endometrial cancer (PAsian- and European-ancestry samples. Conclusions These findings lend support to the hypothesis that genetic polymorphisms in genes involved in the inflammatory pathway may contribute to genetic susceptibility to endometrial cancer. Impact Statement This study adds to the growing evidence that inflammation plays an important role in endometrial carcinogenesis. PMID:23221126

  14. The first pseudo-ternary thiocyanate containing two alkali metals. Synthesis and single-crystal structure of LiK{sub 2}[SCN]{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Reckeweg, Olaf; DiSalvo, Francis J. [Cornell Univ., Ithaca, NY (United States). Baker Lab.

    2016-04-01

    A procedure was empirically developed to prepare the compound LiK{sub 2}[SCN]{sub 3}, which forms colorless, transparent, very fragile, and extremely hygroscopic thin rectangular plates. Its unique crystal structure was determined by single-crystal X-ray diffraction. LiK{sub 2}[SCN]{sub 3} adopts the orthorhombic space group Pna2{sub 1} (no. 33, Z = 4) with the cell parameters a = 1209.32(9), b = 950.85(9), and c = 849.95(6) pm.

  15. Synthesis, crystal structure, and ionic conductivity of a new layered metal phosphate, Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Chul; Kwak, Hyun-Jung [Department of Energy Systems Research, Ajou University, Suwon 16499 (Korea, Republic of); Yoo, Chung-Yul [Advanced Materials & Devices Laboratory, Korea Institute of Energy Research, Daejeon 34129 (Korea, Republic of); Yun, Hoseop [Department of Energy Systems Research, Ajou University, Suwon 16499 (Korea, Republic of); Kim, Seung-Joo, E-mail: sjookim@ajou.ac.kr [Department of Energy Systems Research, Ajou University, Suwon 16499 (Korea, Republic of)

    2016-11-15

    A new layered metal phosphate, Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3}, was synthesized in the form of either a single-crystal or polycrystalline powder using the molten hydroxide flux method or a solid-state reaction, respectively. Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3} crystallizes to the P2{sub 1}/n (Z=4) monoclinic space group with lattice parameters a≈4.95 Å, b≈22.06 Å, c≈8.63 Å, and β≈91.5°. The structure is composed of stacked [LiSrAl(PO{sub 4}){sub 2}] layers alternating regularly with [LiSrPO{sub 4}] layers. In the [LiSrAl(PO{sub 4}){sub 2}] sublattice, the AlO{sub 6} octahedra and PO{sub 4} tetrahedra are tilted cooperatively to form an anionic, corrugated, two-dimensional [Al(PO{sub 4}){sub 2}]{sup 3−} framework that can be regarded as a “distorted-glaserite” structure. The [LiSrPO{sub 4}] sublattice is that of a layered block containing a six-membered ring formed from alternating linkages of LiO{sub 4} and PO{sub 4} tetrahedra. The six-membered rings show a boat-type arrangement with the up(U) or down(D) pointing sequence, UUDUUD. The interspace between the two sublattices generates a two-dimensional pathway for Li{sup +} ion conduction. The impedance measurement indicated that Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3} had a moderate ion conductivity (σ≈1.30×10{sup −4} S cm{sup −1} at 667 K), with an activation energy E{sub a}≈1.02 eV. - Graphical abstract: Polyhedral view of Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3}. Li{sup +} ions are represented by green spheres, Sr atoms by white spheres, AlO{sub 6} groups by octahedra, and PO{sub 4} groups by tetrahedra. - Highlights: • New compound Li{sub 2}Sr{sub 2}Al(PO{sub 4}){sub 3} is reported. • The crystal structure is investigated by single-crystal XRD analysis. • The structure is formed by the alternate stacking of two different sublattices. • Correlation between the crystal structure and ionic conductivity is discussed.

  16. Erstellung eines multimedialen Lernprogramms über die Grundlagen der EKG-Aufzeichnung und Auswertung bei Hund und Katze

    OpenAIRE

    Weigel-Ossiander, Fiona Sarah

    2016-01-01

    Mit EKG Basics wurde ein detailliertes multimediales Lernprogramm über die Grundlagen der Elektrokardiographie bei Hund und Katze erstellt unter besonderer Berücksichtigung von didaktischen und ergonomischen Gesichtspunkten. Da vielen Veterinärmedizinerinnen/Veterinärmedizinern das Erlernen, Verstehen und Interpretieren der Elektrokardiographie schwer fällt, war das Ziel der vorliegenden Arbeit, sowohl Studierenden der Tiermedizin als auch interessierten Tierärztinnen/Tierärzten die Thema...

  17. Über dieses Heft

    Directory of Open Access Journals (Sweden)

    Editors / Herausgeber

    2013-06-01

    Mediendifferenz für das Verständnis von Texten relevant ist: Die Intertextualitätsforschung hat sich schon seit längerem zu einem Interesse für intermediale Beziehungen, Medienwechsel, Transkriptionen erweitert. Diesem Interesse folgt etwa Matthew Boltons Vergleich von Ian McEwans Atonement und der filmischen Umsetzung dieses Romans. Wie überhaupt ein Konzept wie „Immersion in Medien“ sich von literarisch-allegorischen Modellierungen (bei Horacio Quiroga, Jorge Luis Borges und Julio Cortázar zu erzähltheoretischen und schließlich empirisch-psychologischen Kontexten verschiebt, rekonstruiert der Beitrag von Matei Chihaia. Während derart ein in unterschiedlichen Disziplinen aufsteigender ‚Habitus der Medienkompetenz‘ auch zu einer Erweiterung des narratologischen Forschungsinteresses führt, bereichert im Gegenzug der narratologische Zugriff den Umgang mit Medien um Fragestellungen, die für die Erzählforschung spezifisch sind. Und hier ließen sich wohl alle Beiträge der aktuellen Ausgabe anführen, welche die mediale Mannigfaltigkeit auf den Boden einer wissenschaftlichen Disziplin stellen – nur stellvertretend und exemplarisch sei die Titelfrage von Klaus Speidel zitiert: „Can a single picture tell a story?“ Gewiss kann diese Ausgabe nur einen Querschnitt aus dem reichen Feld bieten, in dem sich Erzählen medial auffächert. Dass hierbei das Erzählen im Journalismus und in Computerspielen kaum Erwähnung finden, hängt mit den beiden folgenden Ausgaben von DIEGESIS zusammen: Dort nämlich werden diese Themen im Mittelpunkt stehen. Wenn Sie über Calls for Papers und das Erscheinen künftiger Ausgaben informiert werden wollen, abonnieren Sie bitte unseren Newsletter. Wir freuen uns auf Ihre Beiträge zu den künftigen Themenheften und sind gespannt auf die Rezensionen, die auch in der vorliegenden Ausgabe einen frischen Eindruck von der aktuellen Erzählforschung geben.

  18. Magnetocaloric properties of the hexagonal HoMnO{sub 3} single crystal revisited

    Energy Technology Data Exchange (ETDEWEB)

    Balli, M., E-mail: Mohamed.balli@Usherbrooke.ca [Regroupement québécois sur les matériaux de pointe, Département de physique, Université de Sherbrooke, QC, Canada J1K 2R1 (Canada); Roberge, B.; Vermette, J.; Jandl, S. [Regroupement québécois sur les matériaux de pointe, Département de physique, Université de Sherbrooke, QC, Canada J1K 2R1 (Canada); Fournier, P. [Regroupement québécois sur les matériaux de pointe, Département de physique, Université de Sherbrooke, QC, Canada J1K 2R1 (Canada); Canadian Institute for Advanced Research, Toronto, Ontario, Canada M5G 1Z8 (Canada); Gospodinov, M.M. [Institute of Solid State Physics, Bulgarian Academy of Science, Sofia 1184 (Bulgaria)

    2015-12-01

    Magnetic and magnetocaloric properties of the hexagonal HoMnO{sub 3} single crystal have been revisited. It was found that the magnetocaloric effect shown by HoMnO{sub 3} strongly depends on the crystal orientation in respect to the applied magnetic field. Consequently, a large thermal effect can be induced by spinning the single crystal HoMnO{sub 3} around the a (or b) axis in a constant magnetic field instead of the conventional magnetization–demagnetization process. Under 7 T, the maximum rotating entropy change was evaluated to be about 8 J/kg K. The associated adiabatic temperature change reaches a value of about 5 K. These values are comparable to those of the other oxides exhibiting a large rotating magnetocaloric effect. The presence of both conventional and rotating thermal effects makes the hexagonal HoMnO{sub 3} more interesting from a practical point of view.

  19. Separate Turbo Code and Single Turbo Code Adaptive OFDM Transmissions

    Directory of Open Access Journals (Sweden)

    Lei Ye

    2009-01-01

    Full Text Available This paper discusses the application of adaptive modulation and adaptive rate turbo coding to orthogonal frequency-division multiplexing (OFDM, to increase throughput on the time and frequency selective channel. The adaptive turbo code scheme is based on a subband adaptive method, and compares two adaptive systems: a conventional approach where a separate turbo code is used for each subband, and a single turbo code adaptive system which uses a single turbo code over all subbands. Five modulation schemes (BPSK, QPSK, 8AMPM, 16QAM, and 64QAM are employed and turbo code rates considered are 1/2 and 1/3. The performances of both systems with high (10−2 and low (10−4 BER targets are compared. Simulation results for throughput and BER show that the single turbo code adaptive system provides a significant improvement.

  20. Enhanced visible light photocatalytic performance of polyaniline modified mesoporous single crystal TiO{sub 2} microsphere

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Yaocheng [College of Environmental Science and Engineering, Hunan University, Changsha, 410082 (China); Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082 (China); Tang, Lin, E-mail: tanglin@hnu.edu.cn [College of Environmental Science and Engineering, Hunan University, Changsha, 410082 (China); Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082 (China); Zeng, Guangming, E-mail: zgming@hnu.edu.cn [College of Environmental Science and Engineering, Hunan University, Changsha, 410082 (China); Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082 (China); Dong, Haoran; Yan, Ming; Wang, Jingjing [College of Environmental Science and Engineering, Hunan University, Changsha, 410082 (China); Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082 (China); Hu, Wei [College of Physics and Microelectronics Science, Hunan University, Changsha, 410082 (China); Wang, Jiajia; Zhou, Yaoyu; Tang, Jing [College of Environmental Science and Engineering, Hunan University, Changsha, 410082 (China); Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082 (China)

    2016-11-30

    Highlights: • The mesoporous single crystal microsphere of PANI/MS-TiO{sub 2} improved the light absorption. • The mesoporous structure of MS-TiO{sub 2} can increase the loading amount of PANI. • The synergistic effect between PANI and MS-TiO{sub 2} promoted the separation of charges. • Improved photocatalysis was achieved via PANI modified mesoporous single crystal TiO{sub 2} microsphere. - Abstract: Polyaniline (PANI) modified mesoporous single crystal TiO{sub 2} microsphere (PANI/MS-TiO{sub 2}) with excellent photocatalytic activity was successfully prepared by a simple method of solution evaporation and chemisorption. The X-ray diffraction characterization demonstrated that the whole MS-TiO{sub 2} kept the crystal type of anatase. The nitrogen adsorption-desorption characterization coupled with scanning electron microscopy indicated that the MS-TiO{sub 2} possessed a unique mesoporous structure with high specific surface area, which resulted in the increased load of PANI on the surface of MS-TiO{sub 2} and multiple light reflection in the photocatalyst. The UV–vis diffuse reflectance spectra confirmed that PANI/MS-TiO{sub 2} presented more absorption ability in the visible light range than that of the pristine MS-TiO{sub 2}. The transient photocurrent responses and electrochemical impedance spectroscopy (EIS) indicated the high photo responses and fast photogenerated charge separation efficiency of PANI/MS-TiO{sub 2}. The photocatalytic activity of the PANI/MS-TiO{sub 2} was evaluated by the photodegradation of RhB and MB under visible light irradiation. MS-TiO{sub 2} photocatalyst with different molar ration of PANI had been prepared, and the results showed that the optimal photocatalyst (PANI/MS-TiO{sub 2} (1:40)) exhibited the highest photocatalytic efficiency which is nearly three times as great as that of pristine MS-TiO{sub 2} for the degradation of the RhB and MB under visible light irradiation. The remarkable performance of the PANI/MS-TiO{sub

  1. Hyperoside attenuates hydrogen peroxide-induced L02 cell damage via MAPK-dependent Keap{sub 1}-Nrf{sub 2}-ARE signaling pathway

    Energy Technology Data Exchange (ETDEWEB)

    Xing, Hai-Yan; Liu, Yao; Chen, Jian-Hong; Sun, Feng-Jun; Shi, Hui-Qing [Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038 (China); Xia, Pei-Yuan, E-mail: py_xia@yahoo.com.cn [Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038 (China)

    2011-07-15

    Highlights: {yields} Hyperoside attenuated H{sub 2}O{sub 2}-induced L02 cell damage. {yields} Hyperoside up-regulated HO-1 expression at both mRNA and protein levels. {yields} Hyperoside activated both Nrf{sub 2} nuclear translocation and gene expression. {yields} Hyperoside may inhibit Keap{sub 1} mRNA translation or protein degradation. {yields} Phosphorylation of ERK and p38 is involved in hyperoside-mediated Nrf{sub 2} activation. -- Abstract: The flavonoid hyperoside has been reported to elicit cytoprotection against oxidative stress partly by increasing the activity of antioxidant enzymes, such as glutathione peroxidase, superoxide dismutase and catalase. However, the cellular and molecular mechanisms underlying this effect remain unclear. Here, hepatic L02 cells exposed to H{sub 2}O{sub 2} (100 {mu}M) were used to demonstrate that hyperoside protected cells by significantly inhibiting overproduction of intracellular ROS, depletion of the mitochondrial membrane potential and leakage of lactate dehydrogenase. Hyperoside further enhanced the cellular antioxidant defense system through increasing the activity of heme oxygenase-1 (HO-1), and by up-regulating HO-1 expression. Meanwhile, real time PCR, western blot and immunofluorescence studies revealed that hyperoside stimulated nuclear translocation of the Nrf{sub 2} transcription factor in a dose-dependent manner, and this effect was significantly suppressed by pharmacological inhibition of the mitogen-activated protein kinases (MAPK) p38 and ERK. Collectively, our data provide the first description of the mechanism underlying hyperoside's ability to attenuate H{sub 2}O{sub 2}-induced cell damage, namely this compound interacts with the MAPK-dependent Keap{sub 1}-Nrf{sub 2}-ARE signaling pathway to up-regulate HO-1 expression and enhance intracellular antioxidant activity.

  2. Defect structure of TiS{sub 3} single crystals of the A-ZrSe{sub 3} type

    Energy Technology Data Exchange (ETDEWEB)

    Bolotina, N. B., E-mail: nb-bolotina@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” (Russian Federation); Gorlova, I. G. [Russian Academy of Sciences, Kotel’nikov Institute of Radioengineering and Electronics (Russian Federation); Verin, I. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” (Russian Federation); Titov, A. N. [Russian Academy of Sciences, Mikheev Institute of Metal Physics, Ural Branch (Russian Federation); Arakcheeva, A. V. [Phase Solutions, Co Ltd. (Switzerland)

    2016-11-15

    The defect structure of TiS{sub 3} single crystals of the A-ZrSe{sub 3} type has been determined based on X-ray diffraction data. Shear defects manifest themselves as displacements of ab layers (which can imitate a twin) by ∼0.5a. Regular shears facilitate the formation of a superstructure along the c axis. A model of defect in the layer structure is proposed to explain the atomic displacements at an angle to the layer plane.

  3. Measurement of nucleotide exchange rate constants in single rabbit soleus myofibrils during shortening and lengthening using a fluorescent ATP analog.

    Science.gov (United States)

    Shirakawa, I; Chaen, S; Bagshaw, C R; Sugi, H

    2000-02-01

    The kinetics of displacement of a fluorescent nucleotide, 2'(3')-O-[N[2-[[Cy3]amido]ethyl]carbamoyl]-adenosine 5'-triphosphate (Cy3-EDA-ATP), bound to rabbit soleus muscle myofibrils were studied using flash photolysis of caged ATP. Use of myofibrils from this slow twitch muscle allowed better resolution of the kinetics of nucleotide exchange than previous studies with psoas muscle myofibrils (, Biophys. J. 73:2033-2042). Soleus myofibrils in the presence of Cy3-EDA-nucleotides (Cy3-EDA-ATP or Cy3-EDA-ADP) showed selective fluorescence staining of the A-band. The K(m) for Cy3-EDA-ATP and the K(d) for Cy3-EDA-ADP binding to the myofibril A-band were 1.9 microM and 3.8 microM, respectively, indicating stronger binding of nucleotide to soleus cross-bridges compared to psoas cross-bridges (2.6 microM and 50 microM, respectively). After flash photolysis of caged ATP, the A-band fluorescence of the myofibril in the Cy3-EDA-ATP solution under isometric conditions decayed exponentially with a rate constant of 0.045 +/- 0.007 s(-1) (n = 32) at 10 degrees C, which was about seven times slower than that for psoas myofibrils. When a myofibril was allowed to shorten with a constant velocity, the nucleotide displacement rate constant increased from 0.066 s(-1) (isometric) to 0.14 s(-1) at 20 degrees C with increasing shortening velocity up to 0.1 myofibril length/s (V(max), the shortening velocity under no load was approximately 0. 2 myofibril lengths/s). The rate constant was not significantly affected by an isovelocity stretch of up to 0.1 myofibril lengths/s. These results suggest that the cross-bridge kinetics are not significantly affected at higher strain during lengthening but depend on the lower strain during shortening. These data also indicate that the interaction distance between a cross-bridge and the actin filament is at least 16 nm for a single cycle of the ATPase.

  4. Properties of melt-grown single crystals of 'YB/sub 68/'

    Energy Technology Data Exchange (ETDEWEB)

    Slack, G A; Oliver, D W; Brower, G D; Young, J D [General Electric Co., Schenectady, N.Y. (USA). Research and Development Center

    1977-01-01

    Single crystals of yttrium boride YB/sub n/ with n = 61 +- 3 were grown from the melt. Precision density and lattice parameter measurements indicate a congruent melting point at n = 61.7 and a stoichiometric composition at n = 68. Measurements of elastic constants, acoustic attenuation, electrical resistivity and optical absorption are presented. High resolution transmission electron microscopy reveals a complex crystal structure similar to that found by using X-rays. A comparison of the properties of YB/sub n/ with those of ..beta..-boron show that there are many similarities.

  5. Distinct energetics and closing pathways for DNA polymerase β with 8-oxoG template and different incoming nucleotides

    Directory of Open Access Journals (Sweden)

    Wang Yanli

    2007-02-01

    Full Text Available Abstract Background 8-Oxoguanine (8-oxoG is a common oxidative lesion frequently encountered by DNA polymerases such as the repair enzyme DNA polymerase β (pol β. To interpret in atomic and energetic detail how pol β processes 8-oxoG, we apply transition path sampling to delineate closing pathways of pol β 8-oxoG complexes with dCTP and dATP incoming nucleotides and compare the results to those of the nonlesioned G:dCTP and G:dATPanalogues. Results Our analyses show that the closing pathways of the 8-oxoG complexes are different from one another and from the nonlesioned analogues in terms of the individual transition states along each pathway, associated energies, and the stability of each pathway's closed state relative to the corresponding open state. In particular, the closed-to-open state stability difference in each system establishes a hierarchy of stability (from high to low as G:C > 8-oxoG:C > 8-oxoG:A > G:A, corresponding to -3, -2, 2, 9 kBT, respectively. This hierarchy of closed state stability parallels the experimentally observed processing efficiencies for the four pairs. Network models based on the calculated rate constants in each pathway indicate that the closed species are more populated than the open species for 8-oxoG:dCTP, whereas the opposite is true for 8-oxoG:dATP. Conclusion These results suggest that the lower insertion efficiency (larger Km for dATP compared to dCTP opposite 8-oxoG is caused by a less stable closed-form of pol β, destabilized by unfavorable interactions between Tyr271 and the mispair. This stability of the closed vs. open form can also explain the higher insertion efficiency for 8-oxoG:dATP compared to the nonlesioned G:dATP pair, which also has a higher overall conformational barrier. Our study offers atomic details of the complexes at different states, in addition to helping interpret the different insertion efficiencies of dATP and dCTP opposite 8-oxoG and G.

  6. Self-diffusion of calcium and yttrium in pure and YF/sub 3/-doped CaF/sub 2/ single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kucheria, C.S.

    1979-07-01

    Self-diffusion coefficients for Ca and Y were measured in pure and YF/sub 3/-doped CaF/sub 2/ crystals for dopant levels ranging from 2 to 10 mole %. Diffusion data were analyzed as a function of temperature and as a function of composition. Comparison of Arrhenius relationships for both Ca and Y showed that the activation energy for cation diffusion decreased approximately linearly as the YF/sub 3/ dopant level increased. Atomic jump pathways were considered and the decrease in the activation energy was explained by an increase in the constriction sizes due to Willis cluster formation. Diffusion coefficients for both cations were found to increase approximately linearly with square of the mole percent YF/sub 3/. A comparison of activation energies and diffusion coefficients for both cations in doped crystals indicated that Y required lower activation energy for diffusion than Ca but the diffusion coefficient was also lower for Y compared to Ca. The smaller activation energy for Y was explained by the smaller ionic size of Y, whereas the smaller diffusion coefficient for Y was explained on the basis of highly correlated jumps of Y ions because of interaction between Y/sub Ca/ and V/sub Ca/.

  7. The new 'BerSANS-PC' software for reduction and treatment of small angle neutron scattering data

    International Nuclear Information System (INIS)

    Keiderling, U.

    2002-01-01

    Measurements on small angle neutron scattering (SANS) instruments are typically characterized by a large number of samples, short measurement times for the individual samples, and a frequent change of visiting scientist groups. Besides this, recent advances in instrumentation have led to more frequent measurements of kinetic sequences and a growing interest in analyzing two-dimensional scattering data, these requiring special software tools that enable the users to extract physically relevant information from the scattering data with a minimum of effort. The new 'BerSANS-PC' data-processing software has been developed at the Hahn-Meitner-Institut (HMI) in Berlin, Germany, to meet these requirements and to support an efficiently working guest-user service. Comprising some basic functions of the 'BerSANS' program available at the HMI and other institutes in the past, BerSANS-PC is a completely new development for network-independent use on local PCs with a full-feature graphical interface. (orig.)

  8. Multiple repair pathways mediate cellular tolerance to resveratrol-induced DNA damage.

    Science.gov (United States)

    Liu, Ying; Wu, Xiaohua; Hu, Xiaoqing; Chen, Ziyuan; Liu, Hao; Takeda, Shunichi; Qing, Yong

    2017-08-01

    Resveratrol (RSV) has been reported to exert health benefits for the prevention and treatment of many diseases, including cancer. The anticancer mechanisms of RSV seem to be complex and may be associated with genotoxic potential. To better understand the genotoxic mechanisms, we used wild-type (WT) and a panel of isogenic DNA-repair deficient DT40 cell lines to identify the DNA damage effects and molecular mechanisms of cellular tolerance to RSV. Our results showed that RSV induced significant formation of γ-H2AX foci and chromosome aberrations (CAs) in WT cells, suggesting direct DNA damage effects. Comparing the survival of WT with isogenic DNA-repair deficient DT40 cell lines demonstrated that single strand break repair (SSBR) deficient cell lines of Parp1 -/- , base excision repair (BER) deficient cell lines of Polβ -/- , homologous recombination (HR) mutants of Brca1 -/- and Brca2 -/- and translesion DNA synthesis (TLS) mutants of Rev3 -/- and Rad18 -/- were more sensitive to RSV. The sensitivities of cells were associated with enhanced DNA damage comparing the accumulation of γ-H2AX foci and number of CAs of isogenic DNA-repair deficient DT40 cell lines with WT cells. These results clearly demonstrated that RSV-induced DNA damage in DT40 cells, and multiple repair pathways including BER, SSBR, HR and TLS, play critical roles in response to RSV- induced genotoxicity. Copyright © 2017. Published by Elsevier Ltd.

  9. Spin-glass behavior in single crystals of hetero-metallic magnetic warwickites MgFeBO{sub 4,} Mg{sub 0.5}Co{sub 0.5}FeBO{sub 4,} and CoFeBO{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Arauzo, A., E-mail: aarauzo@unizar.es [Servicio de Medidas Físicas, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza (Spain); Kazak, N.V. [L.V. Kirensky Institute of Physics, SB of RAS, 660036 Krasnoyarsk (Russian Federation); Ivanova, N.B. [Siberian Federal University, 660074 Krasnoyarsk (Russian Federation); Platunov, M.S. [L.V. Kirensky Institute of Physics, SB of RAS, 660036 Krasnoyarsk (Russian Federation); Knyazev, Yu.V. [Siberian Federal University, 660074 Krasnoyarsk (Russian Federation); Bayukov, O.A.; Bezmaternykh, L.N. [L.V. Kirensky Institute of Physics, SB of RAS, 660036 Krasnoyarsk (Russian Federation); Lyubutin, I.S.; Frolov, K.V. [Shubnikov Institute of Crystallography, RAS, 119333 Moscow (Russian Federation); Ovchinnikov, S.G. [L.V. Kirensky Institute of Physics, SB of RAS, 660036 Krasnoyarsk (Russian Federation); Siberian Federal University, 660074 Krasnoyarsk (Russian Federation); Siberian State Aerospace University, 660014 Krasnoyarsk (Russian Federation); Bartolomé, J. [Instituto de Ciencia de Materiales de Aragón, CSIC-Universidad de Zaragoza and Departamento de Física de la Materia Condensada, 50009 Zaragoza (Spain)

    2015-10-15

    Magnetic properties of heterometallic warwickites MgFeBO{sub 4,} Mg{sub 0.5}Co{sub 0.5}FeBO{sub 4,} and CoFeBO{sub 4} are presented, highlighting the effect of Co substitution on the magnetic properties of these compounds. The analysis of magnetization and heat capacity data has shown that these compounds exhibit a spin-glass transition below T{sub SG}=10, 20 and 22 K, respectively. Using zero field ac susceptibility as entanglement witness we find that the low dimensional magnetic behavior above T{sub SG} show quantum entanglement behavior χ(Τ)∝T{sup −α(Τ)} up to T{sub E}≈130 K. The α parameters have been deduced as a function of temperature and Co content, indicating the existence of random singlet phase in this temperature region. Above T{sub E} the paramagnetism is interpreted in terms of non-entangled spins giving rise to Curie–Weiss paramagnetism. The different intra- and inter-ribbon exchange interaction pathways have been calculated within a simple indirect coupling model. It is determined that the triangular motifs in the warwickite structure, together with the competing interactions, induce frustration. The spin-glass character is explained in terms of the substitutional disorder of the Mg, Fe and Co atoms at the two available crystallographic sites, and the frustration induced by the competing interactions. The Co substitution induces uniaxial anisotropy, increases the absolute magnetization and increases the spin-glass freezing temperature. The entanglement behavior is supported in the intermediate phase irrespective of the introduction of anisotropy by the Co substitution. - Highlights: • Spin-glass transition of MgFeBO{sub 4,} Mg{sub 0.5}Co{sub 0.5}FeBO{sub 4,} and CoFeBO{sub 4}. • Anisotropy and transition temperature T{sub SG} increases with Co substitution. • Dynamical scaling theory near T{sub SG} is fulfilled. • Quantum entanglement is observed in between T{sub SG} and T{sub E}=130 K. • Low dimensional random singlet phase

  10. CARD15 single nucleotide polymorphisms 8, 12 and 13 are not increased in ethnic Danes with sarcoidosis

    DEFF Research Database (Denmark)

    Milman, Nils; Nielsen, Ole Haagen; Hviid, Thomas Vauvert F

    2007-01-01

    and SNP13, respectively, were performed by capillary electrophoresis single-strand confirmation polymorphism in 53 patients with histologically verified sarcoidosis and in 103 healthy controls. RESULTS: The frequencies of CARD15 mutations in sarcoidosis patients were: SNP8, 4/106 chromosomes (3.8%); SNP12...... with Crohn's disease. OBJECTIVES: To evaluate whether ethnic Danes with sarcoidosis have an increased frequency of CARD15 mutations compared to healthy control subjects. METHODS: Genotyping for CARD15 mutations R702W, G908R, and L1007fsinsC, also designated single nucleotide polymorphism (SNP) SNP8, SNP12......, 2/106 chromosomes (1.9%); SNP13, 2/106 chromosomes (1.9%); SNP8+SNP12+SNP13, 8/106 chromosomes (7.6%). All 8 patients were heterozygous. The frequencies in controls were: SNP8, 9/206 chromosomes (4.4%); SNP12, 2/206 chromosomes (1.0%); SNP13, 4/206 chromosomes (1.9%); SNP8+SNP12+SNP13, 15...

  11. A common single nucleotide polymorphism can exacerbate long-QT type 2 syndrome leading to sudden infant death

    DEFF Research Database (Denmark)

    Nof, Eyal; Cordeiro, Jonathan M; Pérez, Guillermo J

    2010-01-01

    the mother (both asymptomatic), led to 2 cases of sudden infant death. METHODS AND RESULTS: KCNQ1, KCNH2, SCN5A, KCNE1, KCNE2, CACNA1c, CACNB2b, and KCNJ2 genes were amplified and analyzed by direct sequencing. Functional electrophysiological studies were performed with the single nucleotide polymorphism...... and mutation expressed singly and in combination in Chinese ovary (CHO-K1) and COS-1 cells. An asymptomatic woman presenting after the death of her 2-day-old infant and spontaneous abortion of a second baby in the first trimester was referred for genetic analysis. The newborn infant had nearly incessant...... ventricular tachycardia while in utero and a prolonged QTc (560 ms). The mother was asymptomatic but displayed a prolonged QTc. Genetic screening of the mother revealed a heterozygous nonsense mutation (P926AfsX14) in KCNH2, predicting a stop codon. The father was asymptomatic with a normal QTc but had...

  12. Critical end point of the first-order ferromagnetic transition in a Sm{sub 0.55}(Sr{sub 0.5}Ca{sub 0.5}){sub 0.45}MnO{sub 3} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Radheep, D. Mohan [Centre for High Pressure Research, School of Physics, Bharathidasan University, Tiruchirappalli 620 024 (India); Sarkar, P. [Department of Physics, Serampore College, Serampore 712 201 (India); Arumugam, S. [Centre for High Pressure Research, School of Physics, Bharathidasan University, Tiruchirappalli 620 024 (India); Suryanarayanan, R. [Laboratoire de Physico-Chimie de l' Etat Solide, ICMMO, CNRS, UMR8182, Universite Paris-Sud, 91405 Orsay (France); Mandal, P., E-mail: prabhat.mandal@saha.ac.in [Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Calcutta 700 064 (India)

    2014-09-01

    We report on the magnetic field (H) and hydrostatic pressure (P) dependence of the order of the ferromagnetic (FM) to paramagnetic phase transition in a Sm{sub 0.55}(Sr{sub 0.5}Ca{sub 0.5}){sub 0.45}MnO{sub 3} single crystal. At ambient condition, the system exhibits a first-order FM transition at T{sub C}≈82K (in heating cycle) with strong thermal hysteresis (∼13 K). The application of external H and P increases T{sub C}, suppresses the hysteresis width, and thus weakens the first-order nature of the transition. Our analysis reveals that the hysteresis vanishes and the first-order FM transition becomes a crossover above a critical magnetic field H{sub cr}≈11.5T. The value of H{sub cr} is highest among the manganite family, although the first-order nature of the FM transition is believed to be strongest in Eu{sub 1−x}Sr{sub x}MnO{sub 3}(x≈0.45). - Highlights: • System shows a strong first-order ferromagnetic to paramagnetic phase transition. • Extremely sharp metal–insulator transition at around 82 K. • The value of critical magnetic field at which first-order transition becomes a crossover is highest among manganites. • The nature of transition is sensitive to external perturbations such as magnetic field and pressure.

  13. Are glutathione S transferases involved in DNA damage signalling? Interactions with DNA damage and repair revealed from molecular epidemiology studies

    International Nuclear Information System (INIS)

    Dusinska, Maria; Staruchova, Marta; Horska, Alexandra; Smolkova, Bozena; Collins, Andrew; Bonassi, Stefano; Volkovova, Katarina

    2012-01-01

    Glutathione S-transferases (GSTs) are members of a multigene family of isoenzymes that are important in the control of oxidative stress and in phase II metabolism. Acting non-enzymically, GSTs can modulate signalling pathways of cell proliferation, cell differentiation and apoptosis. Using a molecular epidemiology approach, we have investigated a potential involvement of GSTs in DNA damage processing, specifically the modulation of DNA repair in a group of 388 healthy adult volunteers; 239 with at least 5 years of occupational exposure to asbestos, stone wool or glass fibre, and 149 reference subjects. We measured DNA damage in lymphocytes using the comet assay (alkaline single cell gel electrophoresis): strand breaks (SBs) and alkali-labile sites, oxidised pyrimidines with endonuclease III, and oxidised purines with formamidopyrimidine DNA glycosylase. We also measured GST activity in erythrocytes, and the capacity for base excision repair (BER) in a lymphocyte extract. Polymorphisms in genes encoding three GST isoenzymes were determined, namely deletion of GSTM1 and GSTT1 and single nucleotide polymorphism Ile105Val in GSTP1. Consumption of vegetables and wine correlated negatively with DNA damage and modulated BER. GST activity correlated with oxidised bases and with BER capacity, and differed depending on polymorphisms in GSTP1, GSTT1 and GSTM1. A significantly lower BER rate was associated with the homozygous GSTT1 deletion in all asbestos site subjects and in the corresponding reference group. Multifactorial analysis revealed effects of sex and exposure in GSTP1 Ile/Val heterozygotes but not in Ile/Ile homozygotes. These variants affected also SBs levels, mainly by interactions of GSTP1 genotype with exposure, with sex, and with smoking habit; and by an interaction between sex and smoking. Our results show that GST polymorphisms and GST activity can apparently influence DNA stability and repair of oxidised bases, suggesting a potential new role for these

  14. Are glutathione S transferases involved in DNA damage signalling? Interactions with DNA damage and repair revealed from molecular epidemiology studies

    Energy Technology Data Exchange (ETDEWEB)

    Dusinska, Maria, E-mail: Maria.DUSINSKA@nilu.no [CEE-Health Effects Group, NILU - Norwegian Institute for Air Research, Kjeller (Norway); Staruchova, Marta; Horska, Alexandra [Department of Experimental and Applied Genetics, Slovak Medical University, Bratislava (Slovakia); Smolkova, Bozena [Laboratory of Cancer Genetics, Cancer Research Institute of the Slovak Academy of Sciences, Bratislava (Slovakia); Collins, Andrew [Department of Nutrition, Faculty of Medicine, University of Oslo (Norway); Bonassi, Stefano [Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana, Rome (Italy); Volkovova, Katarina [Department of Experimental and Applied Genetics, Slovak Medical University, Bratislava (Slovakia)

    2012-08-01

    Glutathione S-transferases (GSTs) are members of a multigene family of isoenzymes that are important in the control of oxidative stress and in phase II metabolism. Acting non-enzymically, GSTs can modulate signalling pathways of cell proliferation, cell differentiation and apoptosis. Using a molecular epidemiology approach, we have investigated a potential involvement of GSTs in DNA damage processing, specifically the modulation of DNA repair in a group of 388 healthy adult volunteers; 239 with at least 5 years of occupational exposure to asbestos, stone wool or glass fibre, and 149 reference subjects. We measured DNA damage in lymphocytes using the comet assay (alkaline single cell gel electrophoresis): strand breaks (SBs) and alkali-labile sites, oxidised pyrimidines with endonuclease III, and oxidised purines with formamidopyrimidine DNA glycosylase. We also measured GST activity in erythrocytes, and the capacity for base excision repair (BER) in a lymphocyte extract. Polymorphisms in genes encoding three GST isoenzymes were determined, namely deletion of GSTM1 and GSTT1 and single nucleotide polymorphism Ile105Val in GSTP1. Consumption of vegetables and wine correlated negatively with DNA damage and modulated BER. GST activity correlated with oxidised bases and with BER capacity, and differed depending on polymorphisms in GSTP1, GSTT1 and GSTM1. A significantly lower BER rate was associated with the homozygous GSTT1 deletion in all asbestos site subjects and in the corresponding reference group. Multifactorial analysis revealed effects of sex and exposure in GSTP1 Ile/Val heterozygotes but not in Ile/Ile homozygotes. These variants affected also SBs levels, mainly by interactions of GSTP1 genotype with exposure, with sex, and with smoking habit; and by an interaction between sex and smoking. Our results show that GST polymorphisms and GST activity can apparently influence DNA stability and repair of oxidised bases, suggesting a potential new role for these

  15. Neuronale Korrelate sozialer Interaktion beim Menschen und deren genetische Modulation unter besonderer Berücksichtigung des Spiegelneuronensystems

    OpenAIRE

    Cordes, Andrea

    2013-01-01

    Die in vielen Lebenssituationen über Erfolg und Misserfolg, Sympathie und Antipathie entscheidende, unterschiedlich ausgeprägte Fähigkeit zur sozialen Interaktion ist Gegenstand neurowissenschaftlicher Untersuchungen. Die Versuche einer kortikalen Lokalisierung führten zur Beschreibung des Spiegelneuronensystems (SNS) in Hirnregionen, die sowohl beim Ausführen einer Aktion Aktivität zeigten als auch beim Beobachten derselben beim Gegenüber. Die stärkste Aktivierung dieser Areale wurde bei sch...

  16. Human monocytes undergo excessive apoptosis following temozolomide activating the ATM/ATR pathway while dendritic cells and macrophages are resistant.

    Directory of Open Access Journals (Sweden)

    Martina Bauer

    Full Text Available Immunodeficiency is a severe therapy-limiting side effect of anticancer chemotherapy resulting from sensitivity of immunocompetent cells to DNA damaging agents. A central role in the immune system is played by monocytes that differentiate into macrophages and dendritic cells (DCs. In this study we compared human monocytes isolated from peripheral blood and cytokine matured macrophages and DCs derived from them and assessed the mechanism of toxicity of the DNA methylating anticancer drug temozolomide (TMZ in these cell populations. We observed that monocytes, but not DCs and macrophages, were highly sensitive to the killing effect of TMZ. Studies on DNA damage and repair revealed that the initial DNA incision was efficient in monocytes while the re-ligation step of base excision repair (BER can not be accomplished, resulting in an accumulation of DNA single-strand breaks (SSBs. Furthermore, monocytes accumulated DNA double-strand breaks (DSBs following TMZ treatment, while DCs and macrophages were able to repair DSBs. Monocytes lack the DNA repair proteins XRCC1, ligase IIIα and PARP-1 whose expression is restored during differentiation into macrophages and DCs following treatment with GM-CSF and GM-CSF plus IL-4, respectively. These proteins play a key role both in BER and DSB repair by B-NHEJ, which explains the accumulation of DNA breaks in monocytes following TMZ treatment. Although TMZ provoked an upregulation of XRCC1 and ligase IIIα, BER was not enhanced likely because PARP-1 was not upregulated. Accordingly, inhibition of PARP-1 did not sensitize monocytes, but monocyte-derived DCs in which strong PARP activation was observed. TMZ induced in monocytes the DNA damage response pathways ATM-Chk2 and ATR-Chk1 resulting in p53 activation. Finally, upon activation of the Fas-receptor and the mitochondrial pathway apoptosis was executed in a caspase-dependent manner. The downregulation of DNA repair in monocytes, resulting in their selective

  17. YbNi{sub 4}P{sub 2}. Single crystal growth by the Czochralski method and high-field magnetization measurements

    Energy Technology Data Exchange (ETDEWEB)

    Kliemt, Kristin; Krellner, Cornelius [Goethe-University, Frankfurt (Germany); Foerster, Tobias [HLD, Helmholtz-Zentrum Dresden-Rossendorf, Dresden (Germany); Brando, Manuel [MPI for Chemical Physics of Solids, Dresden (Germany)

    2016-07-01

    We have investigated a new generation of YbNi{sub 4}P{sub 2} single crystals that were grown from a levitating melt by the Czochralski method. With T{sub C}= 0.17 K, this ferromagnetic material has the lowest Curie temperature ever observed among stoichiometric compounds. A quantum critical point occurs in the substitution series YbNi{sub 4}(P{sub 1-x}As{sub x}){sub 2} at x ∼ 0.1. The hybridization between localized f-electrons and the conduction electrons leads to a Fermi-liquid ground state with narrow bands and strongly enhanced effective electronic masses (heavy fermion system, Kondo temperature 8 K). An external magnetic field can split the bands, deform the Fermi surface and simultaneously suppress the Kondo interaction. If such a deformation changes the topology, it is called a Lifshitz transition. Previous thermodynamic and electrical transport studies have found indications for Lifshitz transitions in this Kondo lattice system. We report on results of high-field magnetization measurements at low temperature to further investigate the putative Lifshitz transitions in YbNi{sub 4}P{sub 2}.

  18. Edge structures and properties of triangular antidots in single-layer MoS{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Gan, Li-Yong, E-mail: ganly@swjtu.edu.cn, E-mail: iamyccheng@njtech.edu.cn, E-mail: udo.schwingenschlogl@kaust.edu.sa [Key Laboratory of Advanced Technology of Materials (Ministry of Education), Superconductivity and New Energy R& D Center, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China); Cheng, Yingchun, E-mail: ganly@swjtu.edu.cn, E-mail: iamyccheng@njtech.edu.cn, E-mail: udo.schwingenschlogl@kaust.edu.sa; Huang, Wei [Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials - SICAM, Nanjing Tech University - NanjingTech, 30 South Puzhu Road, Nanjing 211816 (China); Schwingenschlögl, Udo, E-mail: ganly@swjtu.edu.cn, E-mail: iamyccheng@njtech.edu.cn, E-mail: udo.schwingenschlogl@kaust.edu.sa [Physical Science and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900 (Saudi Arabia); Yao, Yingbang [Advanced Nanofabrication and Imaging Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900 (Saudi Arabia); School of Materials and Energy, Guangdong University of Technology, Guangdong 510006 (China); Zhao, Yong [Key Laboratory of Advanced Technology of Materials (Ministry of Education), Superconductivity and New Energy R& D Center, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China); School of Physical Science and Technology, Southwest Jiaotong University, Chengdu, 610031 Sichuan (China); Zhang, Xi-xiang [Physical Science and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900 (Saudi Arabia); Advanced Nanofabrication and Imaging Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900 (Saudi Arabia)

    2016-08-29

    Density functional theory and experiments are employed to shed light on the edge structures of antidots in O etched single-layer MoS{sub 2}. The equilibrium morphology is found to be the zigzag Mo edge with each Mo atom bonded to two O atoms, in a wide range of O chemical potentials. Scanning electron microscopy shows that the orientation of the created triangular antidots is opposite to the triangular shape of the single-layer MoS{sub 2} samples, in agreement with the theoretical predictions. Furthermore, edges induced by O etching turn out to be p-doped, suggesting an effective strategy to realize p-type MoS{sub 2} devices.

  19. Association of single nucleotide polymorphisms with radiation-induced esophagitis

    International Nuclear Information System (INIS)

    Zhang Li; Wang Lvhua; Yang Ming; Ji Wei; Zhao Lujun; Yang Weizhi; Zhou Zongmei; Ou Guangfei; Lin Dongxin

    2008-01-01

    Objective: To evaluate the relationship between single nucleotide polymorphism(SNP) of candidate genes and radiation-induced esophagitis (RIE) in patients with lung cancer. Methods: Between Jan. 2004 and Aug. 2006, 170 patients with pathologically diagnosed lung cancer were enrolled in this study. The total target dose was 45-70 Gy (median 60 Gy). One hundred and thirty-two patients were treated with three-dimensional conformal radiotherapy(3DCRT) and 38 with two-dimensional radiotherapy(2DRT). Forty-one patients received radiotherapy alone, 78 received sequential chemoradiotherapy and 51 received concurrent chemoradiotherapy. Thirty-seven SNPs in 20 DNA repair genes were analyzed by using PCR- based restricted fragment length polymorphism (RFLP). These genes were apoptosis and inflammatory cytokine genes including ATM, ERCC1, XRCC3, XRCCI, XPD, XPC, XPG, NBS1, STK15, ZNF350, ADPRT, TP53, FAS, FASL, CYP2D6*4, CASPASE8, COX2,TGF-β, CD14 and ACE. The endpoint was grade ≥2 R I E. Results: Forty of the 170 patients developed grade ≥2 R I E, including 36 in grade 2 and 4 in grade 3. Univariate analysis revealed that radiation technique and concurrent chemoradiotherapy were statistically significant relatives to the incidence of R I E (P=0.032, 0.049), and both of them had the trend associating with the esophagitis (P=0.072, 0.094). An increased incidence of esophagitis was observed associating with the TGF-β 1 -509T and XPD 751Lys/Lys genotypes (χ 2 =5.65, P=0.017; χ 2 =3.84, P=0.048) in multivariate analysis. Conclusions: Genetic polymorphisms in TGF-β 1 gene and XPD gene have a significant association with radiation-induced esophagitis. (authors)

  20. A study of single nucleotide polymorphism in the ystB gene of Yersinia enterocolitica strains isolated from various wild animal species.

    Science.gov (United States)

    Bancerz-Kisiel, Agata; Szczerba-Turek, Anna; Platt-Samoraj, Aleksandra; Michalczyk, Maria; Szweda, Wojciech

    2017-03-01

    Y. enterocolitica is the causative agent of yersiniosis. The objective of the article was a study of single nucleotide polymorphism in the ystB gene of Y. enterocolitica strains isolated from various wild animal species. High-resolution melting (HRM) analysis was applied to identify single nucleotide polymorphism (SNP) of ystB gene fragments of 88 Y. enterocolitica biotype 1A strains isolated from wild boar, roe deer, red deer and wild ducks. HRM analysis revealed 14 different melting profiles - 4 of them were defined as regular genotypes (G1, G2, G3, G4), whereas 10 as variations. 24 of the examined Y. enterocolitica strains were classified as G1, 18 strains as a G2, 21 strains as a G3, and 15 strains as a G4. Nucleotide sequences classified as G1 revealed 100% similarity with the Y. enterocolitica D88145.1 sequence (NCBI). Analysis of G2 revealed one point mutation - transition T111A. One mutation was also found in G3, but SNP was placed in a different gene region - transition G193A. Two SNPs - transitions G92C and T111A - were identified in G4. Direct sequencing of 10 variations revealed 5 new variants of the ystB nucleotide sequence: V1 - transition G129A (3 strains); V2 - transitions T111A and G193A (2 strains); V3 - transitions C118T and G193A (1 strain); V4 - transitions C141A and G193A (2 strains); and V5 characterized by 19 SNPs: G83A, T93A, A109G, G114T, C116T, A123G, T134C, T142G, T144C, A150C, G162A, T165G, T170G, T174A, T177G, G178A, A179G, A184G and G193A (2 strains). The predominant genotype in isolates from wild ducks was G1; in red deer G2; in wild boar G3; in roe deer G1 and G4. The proposed HRM method could be used to analyze Y. enterocolitica biotype 1A strains isolated from different sources, including humans.

  1. Hall coefficients and optical properties of La/sub 2-//sub x/Sr/sub x/CuO4 single-crystal thin films

    International Nuclear Information System (INIS)

    Suzuki, M.

    1989-01-01

    The low-field Hall coefficient R/sub H/, optical reflectance and transmittance of the La/sub 2-//sub x/Sr/sub x/CuO 4 system with various Sr concentrations from x = 0 to 0.36 are systematically studied using single-crystal thin films epitaxially grown on (100) face SrTiO 3 substrates with the c axis normal to the film surface. For the x range measured, R/sub H/ is positive and decreases more rapidly than that expected from the Sr concentration but more slowly than reported earlier for polycrystalline specimens, indicating anisotropy of R/sub H/. Furthermore, the x dependence indicates deviation from that expected from a simple band model. Within the superconducting composition range, R/sub H/ exhibits characteristic temperature dependence. The optical reflectance spectrum changes from that of a semiconductor at x = 0 to a typical metallic one characterized by the Drude model for x>0.1, indicating the development of itinerant holes in the Cu-O planes. In the optical transmission spectra, an anomalous absorption band is seen in addition to the fundamental absorption corresponding to an energy gap of about 2 eV. This band, which develops with Sr doping, implies an enhancement of the density of states near the Fermi level. Taking these observations into account, the normal-state transport properties are explained with a qualitative consistence

  2. BIG1, a brefeldin A-inhibited guanine nucleotide-exchange protein regulates neurite development via PI3K-AKT and ERK signaling pathways.

    Science.gov (United States)

    Zhou, C; Li, C; Li, D; Wang, Y; Shao, W; You, Y; Peng, J; Zhang, X; Lu, L; Shen, X

    2013-12-19

    The elongation of neuron is highly dependent on membrane trafficking. Brefeldin A (BFA)-inhibited guanine nucleotide-exchange protein 1 (BIG1) functions in the membrane trafficking between the Golgi apparatus and the plasma membrane. BFA, an uncompetitive inhibitor of BIG1 can inhibit neurite outgrowth and polarity development. In this study, we aimed to define the possible role of BIG1 in neurite development and to further investigate the potential mechanism. By immunostaining, we found that BIG1 was extensively colocalized with synaptophysin, a marker for synaptic vesicles in soma and partly in neurites. The amount of both protein and mRNA of BIG1 were up-regulated during rat brain development. BIG1 depletion significantly decreased the neurite length and inhibited the phosphorylation of phosphatidylinositide 3-kinase (PI3K) and protein kinase B (AKT). Inhibition of BIG1 guanine nucleotide-exchange factor (GEF) activity by BFA or overexpression of the dominant-negative BIG1 reduced PI3K and AKT phosphorylation, indicating regulatory effects of BIG1 on PI3K-AKT signaling pathway is dependent on its GEF activity. BIG1 siRNA or BFA treatment also significantly reduced extracellular signal-regulated kinase (ERK) phosphorylation. Overexpression of wild-type BIG1 significantly increased ERK phosphorylation, but the dominant-negative BIG1 had no effect on ERK phosphorylation, indicating the involvement of BIG1 in ERK signaling regulation may not be dependent on its GEF activity. Our result identified a novel function of BIG1 in neurite development. The newly recognized function integrates the function of BIG1 in membrane trafficking with the activation of PI3K-AKT and ERK signaling pathways which are critical in neurite development. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

  3. Optically stimulated luminescence of Tb{sup 3+}/Sm{sup 3+} doubly doped K{sub 2}YF{sub 5} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Camargo, L.; Marcazzo, J.; Santiago, M.; Caselli, E. [Universidad Nacional del Centro de la Provincia de Buenos Aires, Instituto de Fisica Arroyo Seco, Gral. Pinto 399, B7000GHG, Tandil (Argentina); Khaidukov, N. M., E-mail: jmarcass@exa.unicen.edu.ar [Kurnakov Institute of General and Inorganic Chemistry, RAS, Leninskii Prospekt 31, 119991 Moscow (Russian Federation)

    2014-08-15

    In this work optically stimulated luminescence (OSL) properties of K{sub 2}YF{sub 5} crystals doubly doped with Tb{sup 3+} and Sm{sup 3+} ions have been investigated for the first time. OSL responses for different dopant concentration and for optical stimulation with different wavelengths have been analyzed for each compound. Dosimetric properties of the most efficient composition, namely, K{sub 2}YF{sub 5}:1.0 at.% Tb{sup 3+}; 1.0 at.% Sm{sup 3+}, have been studied. Finally, the possible application of this single crystal as OSL dosimeter has been evaluated. (Author)

  4. DNA Three-Way Junction for Differentiation of Single-Nucleotide Polymorphisms with Fluorescent Copper Nanoparticles.

    Science.gov (United States)

    Sun, Feifei; You, Ying; Liu, Jie; Song, Quanwei; Shen, Xiaotong; Na, Na; Ouyang, Jin

    2017-05-23

    A label- and enzyme-free fluorescent sensor for the detection of single-nucleotide polymorphisms (SNPs) at room temperature is proposed, using new copper nanoparticles (CuNPs) as fluorescent reporters. The CuNPs were constructed by using a DNA three-way junction (3WJ) template. In this assay, two complementary adenine/thymine-rich probes can hybridize with the wild-type target simultaneously to construct a 3WJ structure, serving as an efficient scaffold for the generation of CuNPs. However, the CuNPs produce weak fluorescence when the probes bind with a mutant-type target. SNPs can be identified by the difference in fluorescence intensity of the CuNPs. This SNPs detection strategy is straightforward, cost-effective, and avoids the complicated procedures of labeling or enzymatic reactions. The fluorescent sensor is versatile and can be applied to all types of mutation because the probes are programmable. Moreover, the sensor exhibits good detection performance in biological samples. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Proximity effect and Andreev reflection in single-C{sub 60} junctions

    Energy Technology Data Exchange (ETDEWEB)

    Brand, Jonathan; Neel, Nicolas; Kroeger, Joerg [Institut fuer Physik, Technische Universitaet Ilmenau, D-98693 Ilmenau (Germany)

    2016-07-01

    Single C{sub 60} molecules deposited on an ultrathin oxide film on Nb(110) were investigated using a low-temperature scanning tunnelling microscope. Spectroscopy of the differential conductance (dI/dV) in the tunnelling range indicates proximity-induced superconductivity in junctions comprising the oxide layer as well as single C{sub 60} molecules. Andreev reflection is enhanced upon controlled fabrication of tip-surface contacts. With decreasing electrode separation the Bardeen-Cooper-Schrieffer energy gap gradually evolves into a zero-bias peak in dI/dV spectra reflecting the spectroscopic signature of Andreev reflection. The current-voltage characteristics of the tunnelling and contact junctions are well described by the Blonder-Tinkham-Klapwijk theory. Our spectroscopic data evidence the influence of the electrodes' atomic-scale structure on electron transport across normal metal-superconductor interfaces.

  6. Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

    Science.gov (United States)

    Sendorek, Dorota H; Caloian, Cristian; Ellrott, Kyle; Bare, J Christopher; Yamaguchi, Takafumi N; Ewing, Adam D; Houlahan, Kathleen E; Norman, Thea C; Margolin, Adam A; Stuart, Joshua M; Boutros, Paul C

    2018-01-31

    The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly access should be controlled. It is not thought to be possible to re-identify patients from somatic variant data. However, somatic variant detection pipelines can mistakenly identify germline variants as somatic ones, a process called "germline leakage". The rate of germline leakage across different somatic variant detection pipelines is not well-understood, and it is uncertain whether or not somatic variant calls should be considered re-identifiable. To fill this gap, we quantified germline leakage across 259 sets of whole-genome somatic single nucleotide variant (SNVs) predictions made by 21 teams as part of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. The median somatic SNV prediction set contained 4325 somatic SNVs and leaked one germline polymorphism. The level of germline leakage was inversely correlated with somatic SNV prediction accuracy and positively correlated with the amount of infiltrating normal cells. The specific germline variants leaked differed by tumour and algorithm. To aid in quantitation and correction of leakage, we created a tool, called GermlineFilter, for use in public-facing somatic SNV databases. The potential for patient re-identification from leaked germline variants in somatic SNV predictions has led to divergent open data access policies, based on different assessments of the risks. Indeed, a single, well-publicized re-identification event could reshape public perceptions of the values of genomic data sharing. We find that modern somatic SNV prediction pipelines have low germline-leakage rates, which can be further reduced, especially for cloud-sharing, using pre-filtering software.

  7. Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum

    Directory of Open Access Journals (Sweden)

    White Frank F

    2011-07-01

    Full Text Available Abstract Background Eight diverse sorghum (Sorghum bicolor L. Moench accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs. Two strategies were used for DNA library preparation. Missing SNP genotype data were imputed by local haplotype comparison. The effect of library type and genomic diversity on SNP discovery and imputation are evaluated. Results Alignment of eight genome equivalents (6 Gb to the public reference genome revealed 283,000 SNPs at ≥82% confirmation probability. Sequencing from libraries constructed to limit sequencing to start at defined restriction sites led to genotyping 10-fold more SNPs in all 8 accessions, and correctly imputing 11% more missing data, than from semirandom libraries. The SNP yield advantage of the reduced-representation method was less than expected, since up to one fifth of reads started at noncanonical restriction sites and up to one third of restriction sites predicted in silico to yield unique alignments were not sampled at near-saturation. For imputation accuracy, the availability of a genomically similar accession in the germplasm panel was more important than panel size or sequencing coverage. Conclusions A sequence quantity of 3 million 50-base reads per accession using a BsrFI library would conservatively provide satisfactory genotyping of 96,000 sorghum SNPs. For most reliable SNP-genotype imputation in shallowly sequenced genomes, germplasm panels should consist of pairs or groups of genomically similar entries. These results may help in designing strategies for economical genotyping-by-sequencing of large numbers of plant accessions.

  8. Human longevity and variation in DNA damage response and repair

    DEFF Research Database (Denmark)

    Debrabant, Birgit; Soerensen, Mette; Flachsbart, Friederike

    2014-01-01

    others. Data were applied on 592 SNPs from 77 genes involved in nine sub-processes: DNA-damage response, base excision repair (BER), nucleotide excision repair, mismatch repair, non-homologous end-joining, homologous recombinational repair (HRR), RecQ helicase activities (RECQ), telomere functioning...... in genotyping procedures and investigated SNPs, potentially inducing differences in the coverage of gene regions. Specifically, five genes were not covered at all in the German data. Therefore, investigations in additional study populations are needed before final conclusion can be drawn....

  9. High-pressure single-crystal elasticity study of CO{sub 2} across phase I-III transition

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jin S., E-mail: zhang72@illinois.edu; Bass, Jay D. [Department of Geology, University of Illinois, Urbana-Champaign, Illinois 61801 (United States); Shieh, Sean R. [Departments of Earth Sciences and Physics and Astronomy, University of Western Ontario, London, Ontario N6A 5B7 (Canada); Dera, Przemyslaw [Hawaii Institute of Geophysics and Planetology, University of Hawaii at Manoa, Honolulu, Hawaii 96822 (United States); Prakapenka, Vitali [Center for Advanced Radiation Sources, University of Chicago, Chicago, Illinois 60637 (United States)

    2014-04-07

    Sound velocities and elastic moduli of solid single-crystal CO{sub 2} were measured at pressures up to 11.7(3) GPa by Brillouin spectroscopy. The aggregate adiabatic bulk modulus (K{sub S}), shear modulus (G), and their pressure derivatives for CO{sub 2} Phase I are K{sub S0} = 3.4(6) GPa, G{sub 0} = 1.8(2) GPa, (dK{sub S}/dP){sub 0} = 7.8(3), (dG/dP){sub 0} = 2.5(1), (d{sup 2}K{sub S}/dP{sup 2}){sub 0} = −0.23(3) GPa{sup −1}, and (d{sup 2}G/dP{sup 2}){sub 0} = −0.10(1) GPa{sup −1}. A small increase of elastic properties was observed between 9.8(1) and 10.5(3) GPa, in agreement with the CO{sub 2} I-III transition pressure determined from previous x-ray diffraction experiments. Above the transition pressure P{sub T}, we observed a mixture dominated by CO{sub 2}-I, with minor CO{sub 2}-III. The CO{sub 2}-I + III mixture shows slightly increased sound velocities compared to pure CO{sub 2}-I. Elastic anisotropy calculated from the single-crystal elasticity tensor exhibits a decrease with pressure beginning at 7.9(1) GPa, which is lower than P{sub T}. Our results coincide with recent X-ray Raman observations, suggesting that a pressure-induced electronic transition is related to local structural and optical changes.

  10. PARP inhibition versus PARP-1 silencing: different outcomes in terms of single-strand break repair and radiation susceptibility

    International Nuclear Information System (INIS)

    Godon, C.; Cordelieres, F.P.; Giocanti, N.; Megnin-Chanet, F.; Hall, J.; Favaudon, V.; Godon, C.; Giocanti, N.; Megnin-Chanet, F.; Hall, J.; Favaudon, V.; Cordelieres, F.P.; Cordelieres, F.P.; Biard, D.

    2008-01-01

    The consequences of PARP-1 disruption or inhibition on DNA single-strand break repair (SSBR) and radio-induced lethality were determined in synchronized, iso-genic HeLa cells stably silenced or not for poly(ADP-ribose) polymerase-1 (PARP-1) (PARP-1(KD)) or XRCC1 (XRCC1(KD)). PARP-1 inhibition prevented XRCC1-YFP recruitment at sites of 405 nm laser micro irradiation, slowed SSBR 10-fold and triggered the accumulation of large persistent foci of GFP-PARP-1 and GFP-PCNA at photo damaged sites. These aggregates are presumed to hinder the recruitment of other effectors of the base excision repair (BER) pathway.PARP-1 silencing also prevented XRCC1-YFP recruitment but did not lengthen the lifetime of GFP-PCNA foci. Moreover, PARP-1(KD) and XRCC1(KD) cells in S phase completed SSBR as rapidly as controls, while SSBR was delayed in G1. Taken together, the data demonstrate that a PARP-1- and XRCC1-independent SSBR pathway operates when the short patch repair branch of the BER is deficient. Long patch repair is the likely mechanism, as GFP-PCNA recruitment at photo-damaged sites was normal in PARP-1(KD) cells. PARP-1 silencing elicited hyper-radiosensitivity, while radiosensitization by a PARP inhibitor reportedly occurs only in those cells treated in S phase. PARP-1 inhibition and deletion thus have different outcomes in terms of SSBR and radiosensitivity. (authors)

  11. Crystal structures of Ni sup 2 sup + -and Tl sup + -exchanged zeolite X, Ni sub 1 sub 7 Tl sub 5 sub 8 Si sub 1 sub 0 sub 0 Al sub 9 sub 2 O sub 3 sub 8 sub 4 and Ni sub 1 sub 2 Tl sub 6 sub 8 Si sub 1 sub 0 sub 0 Al sub 9 sub 2 O sub 3 sub 8 sub 4

    CERN Document Server

    Song, M K; Kim, Y

    2001-01-01

    The crystal structures of fully dehydrated Ni sup 2 sup + - and Tl sup + -exchanged zeolite X (Ni sub 1 sub 7 Tl sub 5 sub 8 -X, and Ni sub 1 sub 2 Tl sub 6 sub 8 -X; X=Si sub 1 sub 0 sub 0 Al sub 9 sub 2 O sub 3 sub 8 sub 4) have been determined by single-crystal X-ray diffraction techniques in the cubic space group Fd3 at 21(1) .deg. C (a=24.380(4) A, 24.660(4) A, respectively). Their structures have been refined to the final error indices R sub 1 =0.037 and R sub 2 =0.043 with 485 reflections, and R sub 1 =0.039 and R sub 2 =0.040 with 306 reflections, respectively, for which I>3 sigma(I). In Ni sub 1 sub 7 Tl sub 5 sub 8 -X, 17 Ni sup 2 sup + ions per unit cell were found at only two sites: 15 at site I at the center of the hexagonal prism (Ni-O=2.203(9) A). and the remaining 2 at site II near single six-oxygen rings in the supercage (Ni-O=2.16(3) A). Fifty-eight Tl sup + ions were found at five crystallographic sites: 28 at site II (Tl-O=2.626(8) A, 2 at site I' in the sodalite cavity near the hexagonal ...

  12. Heterogeneous activation of H{sub 2}O{sub 2} by defect-engineered TiO{sub 2−x} single crystals for refractory pollutants degradation: A Fenton-like mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ai-Yong, E-mail: ayzhang@hfut.edu.cn; Lin, Tan; He, Yuan-Yi; Mou, Yu-Xuan

    2016-07-05

    Highlights: • Facet- and defect-engineered TiO{sub 2} is proposed for water treatment as Fenton-like catalyst. • The =Ti(III) center serves as lattice shuttle for electron transfer in H{sub 2}O{sub 2} activation. • TiO{sub 2} is promising due to low cost, high abundance, no toxicity and stable performance. - Abstract: The heterogeneous catalyst plays a key role in Fenton-like reaction for advanced oxidation of refractory pollutants in water treatment. Titanium dioxide (TiO{sub 2}) is a typical semiconductor with high industrial importance due to its earth abundance, low cost and no toxicity. In this work, it is found that TiO{sub 2} can heterogeneously activate hydrogen peroxide (H{sub 2}O{sub 2}, E° = 1.78 eV), a common chemical oxidant, to efficiently generate highly-powerful hydroxyl radical, ·OH (E{sup 0} = 2.80 eV), for advanced water treatment, when its crystal shape, exposed facet and oxygen-stoichiometry are finely tuned. The defect-engineered TiO{sub 2} single crystals exposed by high-energy {0 0 1} facets exhibited an excellent Fenton-like activity and stability for degrading typical refractory organic pollutants such as methyl orange and p-nitrophenol. Its defect-centered Fenton-like superiority is mainly attributed to the crystal oxygen-vacancy, single-crystalline structure and exposed polar {0 0 1} facet. Our findings could provide new chance to utilize TiO{sub 2} for Fenton-like technology, and develop novel heterogeneous catalyst for advanced water treatment.

  13. Guanine nucleotide regulation of α1-adrenergic receptors of muscle and kidney eptihelial cells

    International Nuclear Information System (INIS)

    Terman, B.I.; Hughes, R.J.; Slivka, S.R.; Insel, P.A.

    1986-01-01

    The authors have examined the effect of guanine nucleotides on the interaction of adrenergic agents with α 1 -adrenergic receptors of two cell lines, the Madin-Darby Canine Kidney (MDCK) and BC3H-1 muscle cells. While gaunylylimidodiphosphoate (Gpp(NH)p) had no effect on the affinity or the total number of [ -3 H]prazosin binding sites in membranes prepared from these cells, the nucleotide decreased the apparent affinity of the agonist epinephrine in competing for [ 3 H]prazosin binding sites in both cell types. The EC 50 of Gpp(NH)p was ∼100 μM, and a maximal effect was seen at 500 μM. In contrast, 100 μM Gpp(NH)p yielding maximal shifts in binding of epinephrine to β-adrenergic receptors in BC3H-1 cell membranes. Guanine nucleotides were significantly more effective than adenine nucleotides in shifting agonist affinity for the α 1 -receptor and Mg ++ was required to observe a maximal effect. α 1 -receptor agonists activated phosphatidylinositol (PI) hydrolysis in both cell types, but have no direct effect on membrane adenylate cyclase activity. In intact BC3H-1 cells, α 1 -agonists inhibited β-adrenergic cAMP production, an effect which appears in preliminary studies not to result from enhanced phosphodieterase activity. These results show that agonist binding to α 1 -adrenergic receptors in mammalian kidney and muscle cells is regulated by guanine nucleotides. This regulation and inturn transmembrane signalling (PI hydrolysis) by these receptors appear to involve a guanine nucleotide binding (G) protein, which may be different than G/sub s/ and G/sub i/

  14. New paradigms in the repair of oxidative damage in human genome: mechanisms ensuring repair of mutagenic base lesions during replication and involvement of accessory proteins.

    Science.gov (United States)

    Dutta, Arijit; Yang, Chunying; Sengupta, Shiladitya; Mitra, Sankar; Hegde, Muralidhar L

    2015-05-01

    Oxidized bases in the mammalian genome, which are invariably mutagenic due to their mispairing property, are continuously induced by endogenous reactive oxygen species and more abundantly after oxidative stress. Unlike bulky base adducts induced by UV and other environmental mutagens in the genome that block replicative DNA polymerases, oxidatively damaged bases such as 5-hydroxyuracil, produced by oxidative deamination of cytosine in the template strand, do not block replicative polymerases and thus need to be repaired prior to replication to prevent mutation. Following up our earlier studies, which showed that the Nei endonuclease VIII like 1 (NEIL1) DNA glycosylase, one of the five base excision repair (BER)-initiating enzymes in mammalian cells, has enhanced expression during the S-phase and higher affinity for replication fork-mimicking single-stranded (ss) DNA substrates, we recently provided direct experimental evidence for NEIL1's role in replicating template strand repair. The key requirement for this event, which we named as the 'cow-catcher' mechanism of pre-replicative BER, is NEIL1's non-productive binding (substrate binding without product formation) to the lesion base in ss DNA template to stall DNA synthesis, causing fork regression. Repair of the lesion in reannealed duplex is then carried out by NEIL1 in association with the DNA replication proteins. NEIL1 (and other BER-initiating enzymes) also interact with several accessory and non-canonical proteins including the heterogeneous nuclear ribonucleoprotein U and Y-box-binding protein 1 as well as high mobility group box 1 protein, whose precise roles in BER are still obscure. In this review, we have discussed the recent advances in our understanding of oxidative genome damage repair pathways with particular focus on the pre-replicative template strand repair and the role of scaffold factors like X-ray repairs cross-complementing protein 1 and poly (ADP-ribose) polymerase 1 and other accessory

  15. Identification of excitons, trions and biexcitons in single-layer WS{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Plechinger, Gerd; Nagler, Philipp; Kraus, Julia; Paradiso, Nicola; Strunk, Christoph; Schueller, Christian; Korn, Tobias [Institut fuer Experimentelle und Angewandte Physik, Universitaet Regensburg, 93040, Regensburg (Germany)

    2015-08-15

    Single-layer WS{sub 2} is a direct-gap semiconductor showing strong excitonic photoluminescence features in the visible spectral range. Here, we present temperature-dependent photoluminescence measurements on mechanically exfoliated single-layer WS{sub 2}, revealing the existence of neutral and charged excitons at low temperatures as well as at room temperature. By applying a gate voltage, we can electrically control the ratio of excitons and trions and assert a residual n-type doping of our samples. At high excitation densities and low temperatures, an additional peak at energies below the trion dominates the photoluminescence, which we identify as biexciton emission. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome.

    Science.gov (United States)

    Krawitz, Peter M; Schiska, Daniela; Krüger, Ulrike; Appelt, Sandra; Heinrich, Verena; Parkhomchuk, Dmitri; Timmermann, Bernd; Millan, Jose M; Robinson, Peter N; Mundlos, Stefan; Hecht, Jochen; Gross, Manfred

    2014-09-01

    Usher syndrome is an autosomal recessive disorder characterized both by deafness and blindness. For the three clinical subtypes of Usher syndrome causal mutations in altogether 12 genes and a modifier gene have been identified. Due to the genetic heterogeneity of Usher syndrome, the molecular analysis is predestined for a comprehensive and parallelized analysis of all known genes by next-generation sequencing (NGS) approaches. We describe here the targeted enrichment and deep sequencing for exons of Usher genes and compare the costs and workload of this approach compared to Sanger sequencing. We also present a bioinformatics analysis pipeline that allows us to detect single-nucleotide variants, short insertions and deletions, as well as copy number variations of one or more exons on the same sequence data. Additionally, we present a flexible in silico gene panel for the analysis of sequence variants, in which newly identified genes can easily be included. We applied this approach to a cohort of 44 Usher patients and detected biallelic pathogenic mutations in 35 individuals and monoallelic mutations in eight individuals of our cohort. Thirty-nine of the sequence variants, including two heterozygous deletions comprising several exons of USH2A, have not been reported so far. Our NGS-based approach allowed us to assess single-nucleotide variants, small indels, and whole exon deletions in a single test. The described diagnostic approach is fast and cost-effective with a high molecular diagnostic yield.

  17. Formation of SmFe{sub 5}(0001) ordered alloy thin films on Cu(111) single-crystal underlayers

    Energy Technology Data Exchange (ETDEWEB)

    Yabuhara, Osamu; Ohtake, Mitsuru; Nukaga, Yuri; Futamoto, Masaaki [Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551 (Japan); Kirino, Fumiyoshi, E-mail: yabuhara@futamoto.elect.chuo-u.ac.j [Graduate School of Fine Arts, Tokyo National University of Fine Arts and Music, 12-8 Ueno-koen, Taito-ku, Tokyo 110-8714 (Japan)

    2010-01-01

    SmFe{sub 5}(0001) single-crystal thin films are prepared by molecular beam epitaxy employing Cu(111) single-crystal underlayers on MgO(111) substrates. The Cu atoms diffuse into the Sm-Fe layer and substitute the Fe sites in SmFe{sub 5} structure forming an alloy compound of Sm(Fe,Cu){sub 5}. The Sm(Fe,Cu){sub 5} film is more Cu enriched with increasing the substrate temperature. The Cu underlayer plays an important role in assisting the formation of the ordered phase.

  18. Imaging Action Potential in Single Mammalian Neurons by Tracking the Accompanying Sub-Nanometer Mechanical Motion.

    Science.gov (United States)

    Yang, Yunze; Liu, Xian-Wei; Wang, Hui; Yu, Hui; Guan, Yan; Wang, Shaopeng; Tao, Nongjian

    2018-03-28

    Action potentials in neurons have been studied traditionally by intracellular electrophysiological recordings and more recently by the fluorescence detection methods. Here we describe a label-free optical imaging method that can measure mechanical motion in single cells with a sub-nanometer detection limit. Using the method, we have observed sub-nanometer mechanical motion accompanying the action potential in single mammalian neurons by averaging the repeated action potential spikes. The shape and width of the transient displacement are similar to those of the electrically recorded action potential, but the amplitude varies from neuron to neuron, and from one region of a neuron to another, ranging from 0.2-0.4 nm. The work indicates that action potentials may be studied noninvasively in single mammalian neurons by label-free imaging of the accompanying sub-nanometer mechanical motion.

  19. Discriminating a Single Nucleotide Difference for Enhanced miRNA Detection Using Tunable Graphene and Oligonucleotide Nanodevices.

    Science.gov (United States)

    Robertson, Neil M; Hizir, Mustafa Salih; Balcioglu, Mustafa; Wang, Rui; Yavuz, Mustafa Selman; Yumak, Hasan; Ozturk, Birol; Sheng, Jia; Yigit, Mehmet V

    2015-09-15

    In this study we have reported our efforts to address some of the challenges in the detection of miRNAs using water-soluble graphene oxide and DNA nanoassemblies. Purposefully inserting mismatches at specific positions in our DNA (probe) strands shows increasing specificity against our target miRNA, miR-10b, over miR-10a which varies by only a single nucleotide. This increased specificity came at a loss of signal intensity within the system, but we demonstrated that this could be addressed with the use of DNase I, an endonuclease capable of cleaving the DNA strands of the RNA/DNA heteroduplex and recycling the RNA target to hybridize to another probe strand. As we previously demonstrated, this enzymatic signal also comes with an inherent activity of the enzyme on the surface-adsorbed probe strands. To remove this activity of DNase I and the steady nonspecific increase in the fluorescence signal without compromising the recovered signal, we attached a thermoresponsive PEGMA polymer (poly(ethylene glycol) methyl ether methacrylate) to nGO. This smart polymer is able to shield the probes adsorbed on the nGO surface from the DNase I activity and is capable of tuning the detection capacity of the nGO nanoassembly with a thermoswitch at 39 °C. By utilizing probes with multiple mismatches, DNase I cleavage of the DNA probe strands, and the attachment of PEGMA polymers to graphene oxide to block undesired DNase I activity, we were able to detect miR-10b from liquid biopsy mimics and breast cancer cell lines. Overall we have reported our efforts to improve the specificity, increase the sensitivity, and eliminate the undesired enzymatic activity of DNase I on surface-adsorbed probes for miR-10b detection using water-soluble graphene nanodevices. Even though we have demonstrated only the discrimination of miR-10b from miR-10a, our approach can be extended to other short RNA molecules which differ by a single nucleotide.

  20. Can Non-HLA Single Nucleotide Polymorphisms Help Stratify Risk in TrialNet Relatives at Risk for Type 1 Diabetes?

    Science.gov (United States)

    Steck, Andrea K; Xu, Ping; Geyer, Susan; Redondo, Maria J; Antinozzi, Peter; Wentworth, John M; Sosenko, Jay; Onengut-Gumuscu, Suna; Chen, Wei-Min; Rich, Stephen S; Pugliese, Alberto

    2017-08-01

    Genome-wide association studies identified >50 type 1 diabetes (T1D) associated non-human leukocyte antigens (non-HLA) loci. The purpose of this study was to assess the contribution of non-HLA single nucleotide polymorphisms (SNPs) to risk of disease progression. The TrialNet Pathway to Prevention Study follows relatives of T1D patients for development of autoantibodies (Abs) and T1D. Using the Immunochip, we analyzed 53 diabetes-associated, non-HLA SNPs in 1016 Ab-positive, at-risk non-Hispanic white relatives. Effect of SNPs on the development of multiple Abs and T1D. Cox proportional analyses included all substantial non-HLA SNPs, HLA genotypes, relationship to proband, sex, age at initial screening, initial Ab type, and number. Factors involved in progression from single to multiple Abs included age at screening, relationship to proband, HLA genotypes, and rs3087243 (cytotoxic T lymphocyte antigen-4). Significant factors for diabetes progression included age at screening, Ab number, HLA genotypes, rs6476839 [GLIS family zinc finger 3 (GLIS3)], and rs3184504 [SH2B adaptor protein 3 (SH2B3)]. When glucose area under the curve (AUC) was included, factors involved in disease progression included glucose AUC, age at screening, Ab number, relationship to proband, HLA genotypes, rs6476839 (GLIS3), and rs7221109 (CCR7). In stratified analyses by age, glucose AUC, age at screening, sibling, HLA genotypes, rs6476839 (GLIS3), and rs4900384 (C14orf64) were significantly associated with progression to diabetes in participants <12 years old, whereas glucose AUC, sibling, rs3184504 (SH2B3), and rs4900384 (C14orf64) were significant in those ≥12. In conclusion, we identified five non-HLA SNPs associated with increased risk of progression from Ab positivity to disease that may improve risk stratification for prevention trials. Copyright © 2017 by the Endocrine Society

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