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Sample records for adjacent base pairs

  1. Osmium complex binding to mismatched methylcytosine: effect of adjacent bases.

    PubMed

    Nomura, Akiko; Tainaka, Kazuki; Okamoto, Akimitsu

    2009-01-01

    We investigated the efficiency of osmium complex formation at 5-methylcytosine in mismatched DNA duplexes. Osmium complexation was not observed in fully matched duplexes, whereas the complexation site and efficiency in mismatched duplexes depended on the 5'-neighboring base of the 5-methylcytosine. In particular, when the base adjacent to the 5' side of the mismatched base pair was thymine, a unique side reaction was observed. However, the mismatched base pairs did not influence the selectivity of osmium complexation with methylated DNA.

  2. Base pairing and base mis-pairing in nucleic acids

    NASA Technical Reports Server (NTRS)

    Wang, A. H. J.; Rich, A.

    1986-01-01

    In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

  3. Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix.

    PubMed

    Gu, Xiaobo; Mooers, Blaine H M; Thomas, Leonard M; Malone, Joshua; Harris, Steven; Schroeder, Susan J

    2015-10-22

    Consecutive G·U base pairs inside RNA helices can be destabilizing, while those at the ends of helices are thermodynamically stabilizing. To determine if this paradox could be explained by differences in base stacking, we determined the high-resolution (1.32 Å) crystal structure of (5'-GGUGGCUGUU-3')2 and studied three sequences with four consecutive terminal G·U pairs by NMR spectroscopy. In the crystal structure of (5'-GGUGGCUGUU-3')2, the helix is overwound but retains the overall features of A-form RNA. The penultimate base steps at each end of the helix have high base overlap and contribute to the unexpectedly favorable energetic contribution for the 5'-GU-3'/3'-UG-5' motif in this helix position. The balance of base stacking and helical twist contributes to the positional dependence of G·U pair stabilities. The energetic stabilities and similarity to A-form RNA helices suggest that consecutive G·U pairs would be recognized by RNA helix binding proteins, such as Dicer and Ago. Thus, these results will aid future searches for target sites of small RNAs in gene regulation. PMID:26425937

  4. Osmium complexation of mismatched DNA: effect of the bases adjacent to mismatched 5-methylcytosine.

    PubMed

    Nomura, Akiko; Tainaka, Kazuki; Okamoto, Akimitsu

    2009-03-18

    The efficiency of osmium complex formation at 5-methylcytosine in mismatched DNA duplexes is a key point for the design of sequence-specific detection of DNA methylation. Osmium complexation was not observed in fully matched duplexes, whereas the complexation site and efficiency in mismatched duplexes changed depending on the type of 5'-neighboring base of the 5-methylcytosine forming a mismatched base pair. In particular, when the base adjacent to the 5' side of the mismatched base pair was thymine, a unique "side reaction" was observed. However, the nature of the mismatched base pairs in the reaction site did not influence the selectivity of osmium complex formation with methylated DNA.

  5. Report on Pairing-based Cryptography.

    PubMed

    Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

    2015-01-01

    This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed.

  6. Report on Pairing-based Cryptography

    PubMed Central

    Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

    2015-01-01

    This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST’s position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

  7. Report on Pairing-based Cryptography.

    PubMed

    Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

    2015-01-01

    This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

  8. Proteomic profiling of 13 paired ductal infiltrating breast carcinomas and non-tumoral adjacent counterparts.

    PubMed

    Pucci-Minafra, Ida; Cancemi, Patrizia; Marabeti, Maria Rita; Albanese, Nadia Ninfa; Di Cara, Gianluca; Taormina, Pietra; Marrazzo, Antonio

    2007-01-01

    According to recent statistics, breast cancer remains one of the leading causes of death among women in Western countries. Breast cancer is a complex and heterogeneous disease, presently classified into several subtypes according to their cellular origin. Among breast cancer histotypes, infiltrating ductal carcinoma represents the most common and potentially aggressive form. Despite the current progress achieved in early cancer detection and treatment, including the new generation of molecular therapies, there is still need for identification of multiparametric biomarkers capable of discriminating between cancer subtypes and predicting cancer progression for personalized therapies. One established step in this direction is the proteomic strategy, expected to provide enough information on breast cancer profiling. To this aim, in the present study we analyzed 13 breast cancer tissues and their matched non-tumoral tissues by 2-DE. Collectively, we identified 51 protein spots, corresponding to 34 differentially expressed proteins, which may represent promising candidate biomarkers for molecular-based diagnosis of breast cancer and for pattern discovery. The relevance of these proteins as factors contributing to breast carcinogenesis is discussed. PMID:21136615

  9. High base pair opening rates in tracts of GC base pairs.

    PubMed

    Dornberger, U; Leijon, M; Fritzsche, H

    1999-03-12

    Sequence-dependent structural features of the DNA double helix have a strong influence on the base pair opening dynamics. Here we report a detailed study of the kinetics of base pair breathing in tracts of GC base pairs in DNA duplexes derived from 1H NMR measurements of the imino proton exchange rates upon titration with the exchange catalyst ammonia. In the limit of infinite exchange catalyst concentration, the exchange times of the guanine imino protons of the GC tracts extrapolate to much shorter base pair lifetimes than commonly observed for isolated GC base pairs. The base pair lifetimes in the GC tracts are below 5 ms for almost all of the base pairs. The unusually rapid base pair opening dynamics of GC tracts are in striking contrast to the behavior of AT tracts, where very long base pair lifetimes are observed. The implication of these findings for the structural principles governing spontaneous helix opening as well as the DNA-binding specificity of the cytosine-5-methyltransferases, where flipping of the cytosine base has been observed, are discussed.

  10. Automated DNA Base Pair Calling Algorithm

    1999-07-07

    The procedure solves the problem of calling the DNA base pair sequence from two channel electropherogram separations in an automated fashion. The core of the program involves a peak picking algorithm based upon first, second, and third derivative spectra for each electropherogram channel, signal levels as a function of time, peak spacing, base pair signal to noise sequence patterns, frequency vs ratio of the two channel histograms, and confidence levels generated during the run. Themore » ratios of the two channels at peak centers can be used to accurately and reproducibly determine the base pair sequence. A further enhancement is a novel Gaussian deconvolution used to determine the peak heights used in generating the ratio.« less

  11. Radical-pair based avian magnetoreception

    NASA Astrophysics Data System (ADS)

    Procopio, Maria; Ritz, Thorsten

    2014-03-01

    Behavioural experiments suggest that migratory birds possess a magnetic compass sensor able to detect the direction of the geomagnetic. One hypothesis for the basis of this remarkable sensory ability is that the coherent quantum spin dynamics of photoinduced radical pair reactions transduces directional magnetic information from the geomagnetic field into changes of reaction yields, possibly involving the photoreceptor cryptochrome in the birds retina. The suggested radical-pair based avian magnetoreception has attracted attention in the field of quantum biology as an example of a biological sensor which might exploit quantum coherences for its biological function. Investigations on such a spin-based sensor have focussed on uncovering the design features for the design of a biomimetic magnetic field sensor. We study the effects of slow fluctuations in the nuclear spin environment on the directional signal. We quantitatively evaluate the robustness of signals under fluctuations on a timescale longer than the lifetime of a radical pair, utilizing two models of radical pairs. Our results suggest design principles for building a radical-pair based compass sensor that is both robust and highly directional sensitive.

  12. Method for sequencing DNA base pairs

    DOEpatents

    Sessler, Andrew M.; Dawson, John

    1993-01-01

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source.

  13. Signature scheme based on bilinear pairs

    NASA Astrophysics Data System (ADS)

    Tong, Rui Y.; Geng, Yong J.

    2013-03-01

    An identity-based signature scheme is proposed by using bilinear pairs technology. The scheme uses user's identity information as public key such as email address, IP address, telephone number so that it erases the cost of forming and managing public key infrastructure and avoids the problem of user private generating center generating forgery signature by using CL-PKC framework to generate user's private key.

  14. Method for sequencing DNA base pairs

    DOEpatents

    Sessler, A.M.; Dawson, J.

    1993-12-14

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 6 figures.

  15. NMR analysis of base-pair opening kinetics in DNA.

    PubMed

    Szulik, Marta W; Voehler, Markus; Stone, Michael P

    2014-12-12

    Base pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base-pair opening and closing kinetics of individual double-stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state-of-the art techniques and NMR instrumentation, including cryoprobes, is discussed.

  16. Nucleic acid duplexes incorporating a dissociable covalent base pair

    NASA Technical Reports Server (NTRS)

    Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1999-01-01

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

  17. Nucleic acid duplexes incorporating a dissociable covalent base pair.

    PubMed

    Gao, K; Orgel, L E

    1999-12-21

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

  18. Broadband optical parametric amplifier formed by two pairs of adjacent four-wave mixing sidebands in a tellurite microstructured optical fibre

    NASA Astrophysics Data System (ADS)

    Zhang, Lei; Tuan, Tong-Hoang; Kawamura, Harutaka; Nagasaka, Kenshiro; Suzuki, Takenobu; Ohishi, Yasutake

    2016-05-01

    A broadband fibre-optical parametric amplifier (FOPA) operating at a novel wavelength region that is far from the pump wavelength has been demonstrated by exploiting two pairs of adjacent four-wave mixing (FWM) sidebands generated simultaneously in a tellurite microstructured optical fibre (TMOF). Owing to the large nonlinearity of the TMOF and the high pump peak power provided by a picosecond laser, a maximal average gain of 65.1 dB has been obtained. When the FOPA is operated in a saturated state, a flat-gain amplification from 1424 nm to 1459 nm can be achieved. This broadband and high-gain FOPA operating at new wavelength regions far from the pump offers the prospect of all-optical signal processing.

  19. Low-temperature NMR studies on inosine wobble base pairs.

    PubMed

    Janke, Eline M Basílio; Riechert-Krause, Fanny; Weisz, Klaus

    2011-07-01

    Base pairs formed by the inosine nucleoside (I) play an important role in many physiological processes as well as in various DNA technologies. Relative stabilities and favored base pair geometries of free inosine wobble base pairs in aprotic solvents have been determined through (1)H NMR measurements at room temperature and at very low temperatures in a freonic solvent. As indicated by its significantly deshielded imino proton, the Watson-Crick-type I·C base pair forms a remarkably strong NHN hydrogen bond. For the thermodynamically less stable I·A wobble base pair, two configurations of similar population coexist at 133 K in the slow hydrogen bond exchange regime, namely a Watson-Crick(I)-Watson-Crick(A) geometry and a Watson-Crick(I)-Hoogsteen(A) geometry. I·U base pairs are stabilized by two rather weak hydrogen bonds and are significantly disfavored over inosine self-associates in a low-temperature Freon solution. PMID:21644523

  20. Non-target adjacent stimuli classification improves performance of classical ERP-based brain computer interface

    NASA Astrophysics Data System (ADS)

    Ceballos, G. A.; Hernández, L. F.

    2015-04-01

    Objective. The classical ERP-based speller, or P300 Speller, is one of the most commonly used paradigms in the field of Brain Computer Interfaces (BCI). Several alterations to the visual stimuli presentation system have been developed to avoid unfavorable effects elicited by adjacent stimuli. However, there has been little, if any, regard to useful information contained in responses to adjacent stimuli about spatial location of target symbols. This paper aims to demonstrate that combining the classification of non-target adjacent stimuli with standard classification (target versus non-target) significantly improves classical ERP-based speller efficiency. Approach. Four SWLDA classifiers were trained and combined with the standard classifier: the lower row, upper row, right column and left column classifiers. This new feature extraction procedure and the classification method were carried out on three open databases: the UAM P300 database (Universidad Autonoma Metropolitana, Mexico), BCI competition II (dataset IIb) and BCI competition III (dataset II). Main results. The inclusion of the classification of non-target adjacent stimuli improves target classification in the classical row/column paradigm. A gain in mean single trial classification of 9.6% and an overall improvement of 25% in simulated spelling speed was achieved. Significance. We have provided further evidence that the ERPs produced by adjacent stimuli present discriminable features, which could provide additional information about the spatial location of intended symbols. This work promotes the searching of information on the peripheral stimulation responses to improve the performance of emerging visual ERP-based spellers.

  1. 33 CFR 334.1060 - Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... the Oakland Army Base; restricted area. 334.1060 Section 334.1060 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1060 Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. (a) The...

  2. 33 CFR 334.1060 - Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... the Oakland Army Base; restricted area. 334.1060 Section 334.1060 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1060 Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. (a) The...

  3. 33 CFR 334.1060 - Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... the Oakland Army Base; restricted area. 334.1060 Section 334.1060 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1060 Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. (a) The...

  4. 33 CFR 334.1060 - Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... the Oakland Army Base; restricted area. 334.1060 Section 334.1060 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1060 Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. (a) The...

  5. 33 CFR 334.1060 - Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... the Oakland Army Base; restricted area. 334.1060 Section 334.1060 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1060 Oakland Outer Harbor adjacent to the Oakland Army Base; restricted area. (a) The...

  6. Structures of the gauche conformers of somE substituted dimethyl ethers. Effect of adjacent atom lone pairs on methyl group asymmetry

    NASA Astrophysics Data System (ADS)

    Boggs, James E.; Altman, Michael; Cordell, Floyd R.; Dai, Yuanfang

    The complete equilibrium structures of CH 3OCH 3 and of the gauche conformers of CH 30CH 2F, HOCH,F, CH,OCH,Cl and CH,OCH,CN have been determined by ab initio gradient computation at the Hartree-Fock, double zeta-plus-polarization level. The very large asymmetries in CH bond distances previously reported from microwave substitution structures are shown to be non-existent in the equilibrium structures and are presumably artifacts. Small differences, different in direction from those reported from the experiments and nearly an order of magnitude smaller in size, do exist. They reflect three factors: (1) a lengthening of a CH bond which is trans to a lone pair on an adjacent atom, (2) a general shortening of CH bonds originating at a carbon atom bearing a highly electronegative substituent, and (3) a specific interaction in which a CX substituent shortens the nearly parallel CH bond on the other methyl group. The last interaction, not previously reported, is mediated by withdrawal of electron density from the oxygen lone pair which is trans to both groups. Other structural features derived from the microwave studies are supported by the new results. Inclusion of polarization functions in the basis set for oxygen is essential for correct determination of the COC angle and the dihedral angles. The dihedral angles of CH 3OCH 2F and HOCH 2F are not correctly determined by the computation even at this level, although the computed values are improved when d functions are used for oxygen and still more by use of two sets of oxygen d functions. Polarization functions on carbon or on fluorine have no effect on the computed torsional angles. There is no problem in computing the correct dihedral angles with the CI or CN derivatives.

  7. Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs

    NASA Technical Reports Server (NTRS)

    Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.

    2011-01-01

    We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

  8. Base pair opening in three DNA-unwinding elements.

    PubMed

    Coman, Daniel; Russu, Irina M

    2005-05-27

    DNA-unwinding elements are specific base sequences that are located in the origin of DNA replication where they provide the start point for strand separation and unwinding of the DNA double helix. In the present work we have obtained the first characterization of the opening of individual base pairs in DNA-unwinding elements. The three DNA molecules investigated reproduce the 13-mer DNA-unwinding elements present in the Escherichia coli chromosome. The base sequences of the three 13-mers are conserved in the origins of replication of enteric bacterial chromosomes. The exchange of imino protons with solvent protons was measured for each DNA as a function of the concentration of exchange catalyst using nuclear magnetic resonance spectroscopy. The exchange rates provided the rates and the equilibrium constants for opening of individual base pairs in each DNA at 20 degrees C. The results reveal that the kinetics and energetics of the opening reactions for AT/TA base pairs are different in the three DNA-unwinding elements due to long range effects of the base sequence. These differences encompass the AT/TA base pairs that are conserved in various bacterial genomes. Furthermore, a qualitative correlation is observed between the kinetics and energetics of opening of AT/TA base pairs and the location of the corresponding DNA-unwinding element in the origin of DNA replication. PMID:15784615

  9. Effect of base pairing on the electrochemical oxidation of guanine.

    PubMed

    Costentin, Cyrille; Hajj, Viviane; Robert, Marc; Savéant, Jean-Michel; Tard, Cédric

    2010-07-28

    The effect of base pairing by cytosine on the electrochemical oxidation of guanine is examined by means of cyclic voltammetry on carefully purified reactants in a solvent, CHCl(3), which strongly favors the formation of an H-bonded pair. The thermodynamics and kinetics of the oxidation reaction are not strongly influenced by the formation of the pair. They are actually similar to those of the reaction in which 2,6-lutidine, an encumbered base that cannot form a pair with guanine, replaces cytosine. The reaction does not entail a concerted proton-electron mechanism, as attested by the absence of H/D isotope effect. It rather involves the rate-determining formation of the cation radical, followed by its deprotonation and dimerization of the resulting neutral radical in competition with its further oxidation.

  10. Visualizing RNA base-pairing probabilities with RNAbow diagrams.

    PubMed

    Aalberts, Daniel P; Jannen, William K

    2013-04-01

    There are many effective ways to represent a minimum free energy RNA secondary structure that make it easy to locate its helices and loops. It is a greater challenge to visualize the thermal average probabilities of all folds in a partition function sum; dot plot representations are often puzzling. Therefore, we introduce the RNAbows visualization tool for RNA base pair probabilities. RNAbows represent base pair probabilities with line thickness and shading, yielding intuitive diagrams. RNAbows aid in disentangling incompatible structures, allow comparisons between clusters of folds, highlight differences between wild-type and mutant folds, and are also rather beautiful.

  11. How do base-pairing small RNAs evolve?

    PubMed Central

    Updegrove, Taylor B.; Shabalina, Svetlana A.; Storz, Gisela

    2015-01-01

    The increasing numbers of characterized base-pairing small RNAs (sRNAs) and the identification of these regulators in a broad range of bacteria are allowing comparisons between species and explorations of sRNA evolution. In this review, we describe some examples of trans-encoded base-pairing sRNAs that are species-specific and others that are more broadly distributed. We also describe examples of sRNA orthologs where different features are conserved. These examples provide the background for a discussion of mechanisms of sRNA evolution and selective pressures on the sRNAs and their mRNA target(s). PMID:25934120

  12. Partition function and base pairing probabilities of RNA heterodimers

    PubMed Central

    Bernhart, Stephan H; Tafer, Hakim; Mückstein, Ulrike; Flamm, Christoph; Stadler, Peter F; Hofacker, Ivo L

    2006-01-01

    Background RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. Results We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures. Availability RNAcofold is distributed as part of the Vienna RNA Package, . Contact Stephan H. Bernhart – berni@tbi.univie.ac.at PMID:16722605

  13. Adjacency Matrix-Based Transmit Power Allocation Strategies in Wireless Sensor Networks

    PubMed Central

    Consolini, Luca; Medagliani, Paolo; Ferrari, Gianluigi

    2009-01-01

    In this paper, we present an innovative transmit power control scheme, based on optimization theory, for wireless sensor networks (WSNs) which use carrier sense multiple access (CSMA) with collision avoidance (CA) as medium access control (MAC) protocol. In particular, we focus on schemes where several remote nodes send data directly to a common access point (AP). Under the assumption of finite overall network transmit power and low traffic load, we derive the optimal transmit power allocation strategy that minimizes the packet error rate (PER) at the AP. This approach is based on modeling the CSMA/CA MAC protocol through a finite state machine and takes into account the network adjacency matrix, depending on the transmit power distribution and determining the network connectivity. It will be then shown that the transmit power allocation problem reduces to a convex constrained minimization problem. Our results show that, under the assumption of low traffic load, the power allocation strategy, which guarantees minimal delay, requires the maximization of network connectivity, which can be equivalently interpreted as the maximization of the number of non-zero entries of the adjacency matrix. The obtained theoretical results are confirmed by simulations for unslotted Zigbee WSNs. PMID:22346705

  14. Microwave and THz sensing using slab-pair-based metamaterials

    SciTech Connect

    Kenanakis, G.; Shen, Nianhai; Mavidis, Ch.; Katsarakis, N.; Kafesaki, M.; Soukoulis, Costas M.; Economou, E.N.

    2012-10-15

    In this work the sensing capability of an artificial magnetic metamaterial based on pairs of metal slabs is demonstrated, both theoretically and experimentally, in the microwave regime. The demonstration is based on transmission measurements and simulations monitoring the shift of the magnetic resonance frequency as one changes a thin dielectric layer placed between the slabs of the pairs. Strong dependence of the magnetic resonance frequency on both the permittivity and the thickness of the dielectric layer under detection was observed. The sensitivity to the dielectrics′ permittivity (ε) is larger for dielectrics of low ε values, which makes the approach suitable for sensing organic materials also in the THz regime. The capability of our approach for THz sensing is also demonstrated through simulations.

  15. Hydrophobic, Non-Hydrogen-Bonding Bases and Base Pairs in DNA

    PubMed Central

    Schweitzer, Barbara A.; Kool, Eric T.

    2009-01-01

    We report the properties of hydrophobic isosteres of pyrimidines and purines in synthetic DNA duplexes. Phenyl nucleosides 1 and 2 are nonpolar isosteres of the natural thymidine nucleoside, and indole nucleoside 3 is an analog of the complementary purine 2-aminodeoxyadenosine. The nucleosides were incorporated into synthetic oligodeoxynucleotides and were paired against each other and against the natural bases. Thermal denaturation experiments were used to measure the stabilities of the duplexes at neutral pH. It is found that the hydrophobic base analogs are nonselective in pairing with the four natural bases but selective for pairing with each other rather than with the natural bases. For example, compound 2 selectively pairs with itself rather than with A, T, G, or C; the magnitude of this selectivity is found to be 6.5–9.3 °C in Tm or 1.5–1.8 kcal/mol in free energy (25 °C). All possible hydrophobic pairing combinations of 1, 2, and 3 were examined. Results show that the pairing affinity depends on the nature of the pairs and on position in the duplex. The highest affinity pairs are found to be the 1–1 and 2–2 self-pairs and the 1–2 heteropair. The best stabilization occurs when the pairs are placed at the ends of duplexes rather than internally; the internal pairs may be destabilized by imperfect steric mimicry which leads to non-ideal duplex structure. In some cases the hydrophobic pairs are significantly stabilizing to the DNA duplex; for example, when situated at the end of a duplex, the 1–1 pair is more stabilizing than a T–A pair. When situated internally, the affinity of the 1–1 pair is the same as, or slightly better than, the analogous T–T mismatch pair, which is known to have two hydrogen bonds. The studies raise the possibility that hydrogen bonds may not always be required for the formation of stable duplex DNA-like structure. In addition, the results point out the importance of solvation and desolvation in natural base pairing

  16. Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination.

    PubMed

    Takezawa, Yusuke; Nishiyama, Kotaro; Mashima, Tsukasa; Katahira, Masato; Shionoya, Mitsuhiko

    2015-10-12

    A novel bifacial ligand-bearing nucleobase, 5-hydroxyuracil (U(OH) ), which forms both a hydrogen-bonded base pair (U(OH) -A) and a metal-mediated base pair (U(OH) -M-U(OH) ) has been developed. The U(OH) -M-U(OH) base pairs were quantitatively formed in the presence of lanthanide ions such as Gd(III) when U(OH) -U(OH) pairs were consecutively incorporated into DNA duplexes. This result established metal-assisted duplex stabilization as well as DNA-templated assembly of lanthanide ions. Notably, a duplex possessing U(OH) -A base pairs was destabilized by addition of Gd(III) ions. This observation suggests that the hybridization behaviors of the U(OH) -containing DNA strands are altered by metal complexation. Thus, the U(OH) nucleobase with a bifacial base-pairing property holds great promise as a component for metal-responsive DNA materials.

  17. Variable length adjacent partitioning for PTS based PAPR reduction of OFDM signal

    SciTech Connect

    Ibraheem, Zeyid T.; Rahman, Md. Mijanur; Yaakob, S. N.; Razalli, Mohammad Shahrazel; Kadhim, Rasim A.

    2015-05-15

    Peak-to-Average power ratio (PAPR) is a major drawback in OFDM communication. It leads the power amplifier into nonlinear region operation resulting into loss of data integrity. As such, there is a strong motivation to find techniques to reduce PAPR. Partial Transmit Sequence (PTS) is an attractive scheme for this purpose. Judicious partitioning the OFDM data frame into disjoint subsets is a pivotal component of any PTS scheme. Out of the existing partitioning techniques, adjacent partitioning is characterized by an attractive trade-off between cost and performance. With an aim of determining effects of length variability of adjacent partitions, we performed an investigation into the performances of a variable length adjacent partitioning (VL-AP) and fixed length adjacent partitioning in comparison with other partitioning schemes such as pseudorandom partitioning. Simulation results with different modulation and partitioning scenarios showed that fixed length adjacent partition had better performance compared to variable length adjacent partitioning. As expected, simulation results showed a slightly better performance of pseudorandom partitioning technique compared to fixed and variable adjacent partitioning schemes. However, as the pseudorandom technique incurs high computational complexities, adjacent partitioning schemes were still seen as favorable candidates for PAPR reduction.

  18. Physics of base-pairing dynamics in DNA

    NASA Astrophysics Data System (ADS)

    Manghi, Manoel; Destainville, Nicolas

    2016-05-01

    As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque-driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain orientational degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain orientational degrees of freedom can be integrated out, and the quasi-static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

  19. Medical image classification using spatial adjacent histogram based on adaptive local binary patterns.

    PubMed

    Liu, Dong; Wang, Shengsheng; Huang, Dezhi; Deng, Gang; Zeng, Fantao; Chen, Huiling

    2016-05-01

    Medical image recognition is an important task in both computer vision and computational biology. In the field of medical image classification, representing an image based on local binary patterns (LBP) descriptor has become popular. However, most existing LBP-based methods encode the binary patterns in a fixed neighborhood radius and ignore the spatial relationships among local patterns. The ignoring of the spatial relationships in the LBP will cause a poor performance in the process of capturing discriminative features for complex samples, such as medical images obtained by microscope. To address this problem, in this paper we propose a novel method to improve local binary patterns by assigning an adaptive neighborhood radius for each pixel. Based on these adaptive local binary patterns, we further propose a spatial adjacent histogram strategy to encode the micro-structures for image representation. An extensive set of evaluations are performed on four medical datasets which show that the proposed method significantly improves standard LBP and compares favorably with several other prevailing approaches. PMID:27058283

  20. Medical image classification using spatial adjacent histogram based on adaptive local binary patterns.

    PubMed

    Liu, Dong; Wang, Shengsheng; Huang, Dezhi; Deng, Gang; Zeng, Fantao; Chen, Huiling

    2016-05-01

    Medical image recognition is an important task in both computer vision and computational biology. In the field of medical image classification, representing an image based on local binary patterns (LBP) descriptor has become popular. However, most existing LBP-based methods encode the binary patterns in a fixed neighborhood radius and ignore the spatial relationships among local patterns. The ignoring of the spatial relationships in the LBP will cause a poor performance in the process of capturing discriminative features for complex samples, such as medical images obtained by microscope. To address this problem, in this paper we propose a novel method to improve local binary patterns by assigning an adaptive neighborhood radius for each pixel. Based on these adaptive local binary patterns, we further propose a spatial adjacent histogram strategy to encode the micro-structures for image representation. An extensive set of evaluations are performed on four medical datasets which show that the proposed method significantly improves standard LBP and compares favorably with several other prevailing approaches.

  1. Base pairing properties of O/sup 6/-methylguanine

    SciTech Connect

    Williams, L.D.; Shaw, B.R.

    1986-05-01

    Alkyl adducts at the O/sup 6/ position of guanine are understood to be particularly important in the process of mutagenesis. The hydrogen bonding interactions of O/sup 6/-methylguanine (O/sup 6/MeG) with potential base complements in chloroform-d have been investigated by /sup 1/H NMR. For these studies, the authors have employed nucleosides with ribose hydroxyls blocked by triisopropylsilyl groups. The authors have seen that O/sup 6/MeG forms a mispair with thymine (T). However, only under certain circumstances does O/sup 6/MeG interact with cytosine (C). Although no observable interaction occurs between unprotonated C and O/sup 6/MeG, protonated C does base pair with O/sup 6/MeG. Assuming that RNA and DNA polymerases incorporate the physiologically predominant (unionized) form of each base, which may then be protonated, the data accounts both for the coding preference of O/sup 6/MeG for T and for the relatively high stability of the O/sup 6/MeG:C base pair in oligonucleotides.

  2. Optimal technique of linear accelerator-based stereotactic radiosurgery for tumors adjacent to brainstem.

    PubMed

    Chang, Chiou-Shiung; Hwang, Jing-Min; Tai, Po-An; Chang, You-Kang; Wang, Yu-Nong; Shih, Rompin; Chuang, Keh-Shih

    2016-01-01

    Stereotactic radiosurgery (SRS) is a well-established technique that is replacing whole-brain irradiation in the treatment of intracranial lesions, which leads to better preservation of brain functions, and therefore a better quality of life for the patient. There are several available forms of linear accelerator (LINAC)-based SRS, and the goal of the present study is to identify which of these techniques is best (as evaluated by dosimetric outcomes statistically) when the target is located adjacent to brainstem. We collected the records of 17 patients with lesions close to the brainstem who had previously been treated with single-fraction radiosurgery. In all, 5 different lesion catalogs were collected, and the patients were divided into 2 distance groups-1 consisting of 7 patients with a target-to-brainstem distance of less than 0.5cm, and the other of 10 patients with a target-to-brainstem distance of ≥ 0.5 and < 1cm. Comparison was then made among the following 3 types of LINAC-based radiosurgery: dynamic conformal arcs (DCA), intensity-modulated radiosurgery (IMRS), and volumetric modulated arc radiotherapy (VMAT). All techniques included multiple noncoplanar beams or arcs with or without intensity-modulated delivery. The volume of gross tumor volume (GTV) ranged from 0.2cm(3) to 21.9cm(3). Regarding the dose homogeneity index (HIICRU) and conformity index (CIICRU) were without significant difference between techniques statistically. However, the average CIICRU = 1.09 ± 0.56 achieved by VMAT was the best of the 3 techniques. Moreover, notable improvement in gradient index (GI) was observed when VMAT was used (0.74 ± 0.13), and this result was significantly better than those achieved by the 2 other techniques (p < 0.05). For V4Gy of brainstem, both VMAT (2.5%) and IMRS (2.7%) were significantly lower than DCA (4.9%), both at the p < 0.05 level. Regarding V2Gy of normal brain, VMAT plans had attained 6.4 ± 5%; this was significantly better (p < 0.05) than

  3. Direct observation of base-pair stepping by RNA polymerase

    NASA Astrophysics Data System (ADS)

    Abbondanzieri, Elio A.; Greenleaf, William J.; Shaevitz, Joshua W.; Landick, Robert; Block, Steven M.

    2005-11-01

    During transcription, RNA polymerase (RNAP) moves processively along a DNA template, creating a complementary RNA. Here we present the development of an ultra-stable optical trapping system with ångström-level resolution, which we used to monitor transcriptional elongation by single molecules of Escherichia coli RNAP. Records showed discrete steps averaging 3.7 +/- 0.6Å, a distance equivalent to the mean rise per base found in B-DNA. By combining our results with quantitative gel analysis, we conclude that RNAP advances along DNA by a single base pair per nucleotide addition to the nascent RNA. We also determined the force-velocity relationship for transcription at both saturating and sub-saturating nucleotide concentrations; fits to these data returned a characteristic distance parameter equivalent to one base pair. Global fits were inconsistent with a model for movement incorporating a power stroke tightly coupled to pyrophosphate release, but consistent with a brownian ratchet model incorporating a secondary NTP binding site.

  4. Direct observation of base-pair stepping by RNA polymerase.

    PubMed

    Abbondanzieri, Elio A; Greenleaf, William J; Shaevitz, Joshua W; Landick, Robert; Block, Steven M

    2005-11-24

    During transcription, RNA polymerase (RNAP) moves processively along a DNA template, creating a complementary RNA. Here we present the development of an ultra-stable optical trapping system with ångström-level resolution, which we used to monitor transcriptional elongation by single molecules of Escherichia coli RNAP. Records showed discrete steps averaging 3.7 +/- 0.6 A, a distance equivalent to the mean rise per base found in B-DNA. By combining our results with quantitative gel analysis, we conclude that RNAP advances along DNA by a single base pair per nucleotide addition to the nascent RNA. We also determined the force-velocity relationship for transcription at both saturating and sub-saturating nucleotide concentrations; fits to these data returned a characteristic distance parameter equivalent to one base pair. Global fits were inconsistent with a model for movement incorporating a power stroke tightly coupled to pyrophosphate release, but consistent with a brownian ratchet model incorporating a secondary NTP binding site.

  5. Modelling proton tunnelling in the adenine-thymine base pair.

    PubMed

    Godbeer, A D; Al-Khalili, J S; Stevenson, P D

    2015-05-21

    The energies of the canonical (standard, amino-keto) and tautomeric (non-standard, imino-enol) charge-neutral forms of the adenine-thymine base pair (A-T and A*-T*, respectively) are calculated using density functional theory. The reaction pathway is then computed using a transition state search to provide the asymmetric double-well potential minima along with the barrier height and shape, which are combined to create the potential energy surface using a polynomial fit. The influence of quantum tunnelling on proton transfer within a base pair H-bond (modelled as the DFT deduced double-well potential) is then investigated by solving the time-dependent master equation for the density matrix. The effect on a quantum system by its surrounding water molecules is explored via the inclusion of a dissipative Lindblad term in the master equation, in which the environment is modelled as a heat bath of harmonic oscillators. It is found that quantum tunnelling, due to transitions to higher energy eigenstates with significant amplitudes in the shallow (tautomeric) side of the potential, is unlikely to be a significant mechanism for the creation of adenine-thymine tautomers within DNA, with thermally assisted coupling of the environment only able to boost the tunnelling probability to a maximum of 2 × 10(-9). This is barely increased for different choices of the starting wave function or when the geometry of the potential energy surface is varied.

  6. Using Pair Programming to Teach CAD Based Engineering Graphics

    ERIC Educational Resources Information Center

    Leland, Robert P.

    2010-01-01

    Pair programming was introduced into a course in engineering graphics that emphasizes solid modeling using SolidWorks. In pair programming, two students work at a single computer, and periodically trade off roles as driver (hands on the keyboard and mouse) and navigator (discuss strategy and design issues). Pair programming was used in a design…

  7. Detection of base-pair mismatches in DNA using graphene-based nanopore device

    NASA Astrophysics Data System (ADS)

    Kundu, Sourav; Karmakar, S. N.

    2016-04-01

    We present a unique way to detect base-pair mismatches in DNA, leading to a different epigenetic disorder by the method of nanopore sequencing. Based on a tight-binding formulation of a graphene-based nanopore device, using the Green’s function approach we study the changes in the electronic transport properties of the device as we translocate a double-stranded DNA through the nanopore embedded in a zigzag graphene nanoribbon. In the present work we are not only successful in detecting the usual AT and GC pairs but also a set of possible mismatches in the complementary base pairing.

  8. Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm.

    PubMed

    Sadeghi, Mehdi; Parto, Sahar; Arab, Shahriar; Ranjbar, Bijan

    2005-06-20

    We have used a statistical approach for protein secondary structure prediction based on information theory and simultaneously taking into consideration pairwise residue types and conformational states. Since the prediction of residue secondary structure by one residue window sliding make ambiguity in state prediction, we used a dynamic programming algorithm to find the path with maximum score. A score system for residue pairs in particular conformations is derived for adjacent neighbors up to ten residue apart in sequence. The three state overall per-residue accuracy, Q3, of this method in a jackknife test with dataset created from PDBSELECT is more than 70%.

  9. Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.

    PubMed

    Sponer, Judit E; Spacková, Nad'a; Kulhanek, Petr; Leszczynski, Jerzy; Sponer, Jirí

    2005-03-17

    Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions. PMID:16838999

  10. A Multiscale Modeling Demonstration Based on the Pair Correlation Function

    SciTech Connect

    Gao, Carrie Y; Nicholson, Don M; Keffer, David; Edwards, Brian J

    2008-01-01

    For systems with interatomic interactions that are well described by pair-wise potentials, the pair correlation function provides a vehicle for passing information from the molecular level to the macroscopic level of description. In this work, we present a complete demonstration of the use of the pair correlation function to simulate a fluid at the molecular and macroscopic levels. At the molecular level, we describe a monatomic fluid using the Ornstein-Zernike integral equation theory closed with the Percus-Yevick approximation. We show that all of the required thermodynamic properties can be evaluated knowing the pair correlation function. At the macroscopic level, we perform a multiscale simulation with macroscopic evolution equations for the mass, momentum, temperature, and pair correlation function, using molecular-level simulation to provide the boundary conditions. We perform a self-consistency check by comparing the pair correlation function that evolved from the multiscale simulation with the one evaluated at the molecular-level; excellent agreement is achieved.

  11. Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs

    SciTech Connect

    Wu, Yuan-Yan; Bao, Lei; Zhang, Xi; Tan, Zhi-Jie

    2015-03-28

    Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5–50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length l{sub p} of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with l{sub p} ∼ 50 nm.

  12. Plasmon switching effect based on graphene nanoribbon pair arrays

    NASA Astrophysics Data System (ADS)

    Liu, Dan; Wu, Lingxi; Liu, Qiong; Zhou, Renlong; Xie, Suxia; Chen, Jiangjiamin; Wu, Mengxiong; Zeng, Lisan

    2016-10-01

    We theoretically demonstrate the existence of plasmon switching effect in graphene nanostructure. By using finite-difference time-domain (FDTD) method, the plasmon resonance modes are studied in graphene nanoribbon pair arrays with the change of Fermi level, graphene width, and carrier mobility. It is found that the Fermi level and graphene width play an important role in changing the distribution of electric energy on different graphene nanoribbons, resulting in a significant plasmon switching effect. Moreover, we study the characteristic of resonance mode of one graphene ribbon by using glass rod with different shape. The effect of kerr material sandwiched between graphene nanoribbon pair is also considered.

  13. Raising the barrier for photoinduced DNA charge injection with a cyclohexyl artificial base pair.

    PubMed

    Singh, Arunoday P N; Harris, Michelle A; Young, Ryan M; Miller, Stephen A; Wasielewski, Michael R; Lewis, Frederick D

    2015-01-01

    The effects of an artificial cyclohexyl base pair on the quantum yields of fluorescence and dynamics of charge separation and charge recombination have been investigated for several synthetic DNA hairpins. The hairpins possess stilbenedicarboxamide, perylenediimide, or naphthalenediimide linkers and base-paired stems. In the absence of the artificial base pair hole injection into both adenine and guanine purine bases is exergonic and irreversible, except in the case of stilbene with adenine for which it is slightly endergonic and reversible. Insertion of the artificial base pair renders hole injection endergonic or isoergonic except in the case of the powerful naphthalene acceptor for which it remains exergonic. Both hole injection and charge recombination are slower for the naphthalene acceptor in the presence of the artificial base pair than in its absence. The effect of an artificial base pair on charge separation and charge recombination in hairpins possessing stilbene and naphthalene acceptor linkers and a stilbenediether donor capping group has also been investigated. In the case of the stilbene acceptor-stilbene donor capped hairpins photoinduced charge separation across six base pairs is efficient in the absence of the artificial base pair but does not occur in its presence. In the case of the naphthalene acceptor-stilbene donor capped hairpins the artificial base pair slows but does not stop charge separation and charge recombination, leading to the formation of long-lived charge separated states. PMID:26442603

  14. The Simplified Aircraft-Based Paired Approach With the ALAS Alerting Algorithm

    NASA Technical Reports Server (NTRS)

    Perry, Raleigh B.; Madden, Michael M.; Torres-Pomales, Wilfredo; Butler, Ricky W.

    2013-01-01

    This paper presents the results of an investigation of a proposed concept for closely spaced parallel runways called the Simplified Aircraft-based Paired Approach (SAPA). This procedure depends upon a new alerting algorithm called the Adjacent Landing Alerting System (ALAS). This study used both low fidelity and high fidelity simulations to validate the SAPA procedure and test the performance of the new alerting algorithm. The low fidelity simulation enabled a determination of minimum approach distance for the worst case over millions of scenarios. The high fidelity simulation enabled an accurate determination of timings and minimum approach distance in the presence of realistic trajectories, communication latencies, and total system error for 108 test cases. The SAPA procedure and the ALAS alerting algorithm were applied to the 750-ft parallel spacing (e.g., SFO 28L/28R) approach problem. With the SAPA procedure as defined in this paper, this study concludes that a 750-ft application does not appear to be feasible, but preliminary results for 1000-ft parallel runways look promising.

  15. Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency

    PubMed Central

    2010-01-01

    Background Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies. Results Among the discarded data, we found that 23.7 ± 3.9% of singletons and 14.1 ± 1.0% of contigs were assigned to taxa. The recovery rates for singletons were higher than those for contigs. The Pearson correlation coefficient revealed a high degree of similarity (0.94 ± 0.03 at the phylum rank and 0.80 ± 0.11 at the family rank) between the proposed taxonomic binning approach and those reported in original studies. In addition, an evaluation using simulated data demonstrated the reliability of the proposed approach. Conclusions Our findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing. In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes. PMID:21083935

  16. Mutation analysis of the base-pair connecting two functional modules in the DSL ribozyme.

    PubMed

    Ishikawa, Junya; Furuta, Hiroyuki; Ikawa, Yoshiya

    2008-01-01

    The class DSL ribozyme is one of artificial RNA enzymes generated by module-based molecular design. In the structure of this ribozyme, two most important functional modules are connected by a U-A base-pair. We have examined the possible importance of this base-pair by site-directed mutation experiments using the DSL-1S ribozyme and its derivative possessing altered modular organization. The analysis indicated that the DSL-1S ribozyme preferred U-A pair at the positions whereas the derivative preferred A-U pair.

  17. A comprehensive classification of nucleic acid structural families based on strand direction and base pairing.

    PubMed Central

    Lavery, R; Zakrzewska, K; Sun, J S; Harvey, S C

    1992-01-01

    We propose a classification of DNA structures formed from 1 to 4 strands, based only on relative strand directions, base to strand orientation and base pairing geometries. This classification and its associated notation enable all nucleic acids to be grouped into structural families and bring to light possible structures which have not yet been observed experimentally. It also helps in understanding transitions between families and can assist in the design of multistrand structures. PMID:1383936

  18. Alternative radical pairs for cryptochrome-based magnetoreception.

    PubMed

    Lee, Alpha A; Lau, Jason C S; Hogben, Hannah J; Biskup, Till; Kattnig, Daniel R; Hore, P J

    2014-06-01

    There is growing evidence that the remarkable ability of animals, in particular birds, to sense the direction of the Earth's magnetic field relies on magnetically sensitive photochemical reactions of the protein cryptochrome. It is generally assumed that the magnetic field acts on the radical pair [FAD•- TrpH•+] formed by the transfer of an electron from a group of three tryptophan residues to the photo-excited flavin adenine dinucleotide cofactor within the protein. Here, we examine the suitability of an [FAD•- Z•] radical pair as a compass magnetoreceptor, where Z• is a radical in which the electron spin has no hyperfine interactions with magnetic nuclei, such as hydrogen and nitrogen. Quantum spin dynamics simulations of the reactivity of [FAD•- Z•] show that it is two orders of magnitude more sensitive to the direction of the geomagnetic field than is [FAD•- TrpH•+] under the same conditions (50 µT magnetic field, 1 µs radical lifetime). The favourable magnetic properties of [FAD•- Z•] arise from the asymmetric distribution of hyperfine interactions among the two radicals and the near-optimal magnetic properties of the flavin radical. We close by discussing the identity of Z• and possible routes for its formation as part of a spin-correlated radical pair with an FAD radical in cryptochrome. PMID:24671932

  19. Database of non-canonical base pairs found in known RNA structures

    NASA Technical Reports Server (NTRS)

    Nagaswamy, U.; Voss, N.; Zhang, Z.; Fox, G. E.

    2000-01-01

    Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

  20. Fixed-Base Comb with Window-Non-Adjacent Form (NAF) Method for Scalar Multiplication

    PubMed Central

    Seo, Hwajeong; Kim, Hyunjin; Park, Taehwan; Lee, Yeoncheol; Liu, Zhe; Kim, Howon

    2013-01-01

    Elliptic curve cryptography (ECC) is one of the most promising public-key techniques in terms of short key size and various crypto protocols. For this reason, many studies on the implementation of ECC on resource-constrained devices within a practical execution time have been conducted. To this end, we must focus on scalar multiplication, which is the most expensive operation in ECC. A number of studies have proposed pre-computation and advanced scalar multiplication using a non-adjacent form (NAF) representation, and more sophisticated approaches have employed a width-w NAF representation and a modified pre-computation table. In this paper, we propose a new pre-computation method in which zero occurrences are much more frequent than in previous methods. This method can be applied to ordinary group scalar multiplication, but it requires large pre-computation table, so we combined the previous method with ours for practical purposes. This novel structure establishes a new feature that adjusts speed performance and table size finely, so we can customize the pre-computation table for our own purposes. Finally, we can establish a customized look-up table for embedded microprocessors. PMID:23881143

  1. DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration

    NASA Astrophysics Data System (ADS)

    Ferreira, Izabela; Amarante, Tauanne D.; Weber, Gerald

    2015-11-01

    DNA base pairs are known to open more easily at the helix terminal, a process usually called end fraying, the details of which are still poorly understood. Here, we present a mesoscopic model calculation based on available experimental data where we consider separately the terminal base pairs of a DNA duplex. Our results show an important reduction of hydrogen bond strength for terminal cytosine-guanine (CG) base pairs which is uniform over the whole range of salt concentrations, while for AT base pairs, we obtain a nearly 1/3 reduction but only at low salt concentrations. At higher salt concentrations, terminal adenine-thymine (AT) pair has almost the same hydrogen bond strength than interior bases. The calculated terminal stacking interaction parameters display some peculiarly contrasting behavior. While there is mostly no perceptible difference to internal stacking, for some cases, we observe an unusually strong dependence with salt concentration which does not appear follow any pattern or trend.

  2. Functional renormalization-group study of the pairing symmetry and pairing mechanism of the FeAs-based high-temperature superconductor.

    PubMed

    Wang, Fa; Zhai, Hui; Ran, Ying; Vishwanath, Ashvin; Lee, Dung-Hai

    2009-01-30

    We apply the fermion functional renormalization-group method to determine the pairing symmetry and pairing mechanism of the FeAs-Based materials. Within a five band model with pure repulsive interactions, we find an electronic-driven superconducting pairing instability. For the doping and interaction parameters we have examined, extended s wave, whose order parameter takes on opposite sign on the electron and hole pockets, is always the most favorable pairing symmetry. The pairing mechanism is the inter-Fermi-surface Josephson scattering generated by the antiferromagnetic correlation.

  3. The Impact of a Peer-Learning Agent Based on Pair Programming in a Programming Course

    ERIC Educational Resources Information Center

    Han, Keun-Woo; Lee, EunKyoung; Lee, YoungJun

    2010-01-01

    This paper analyzes the educational effects of a peer-learning agent based on pair programming in programming courses. A peer-learning agent system was developed to facilitate the learning of a programming language through the use of pair programming strategies. This system is based on the role of a peer-learning agent from pedagogical and…

  4. The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation

    PubMed Central

    Yamaguchi, Hiroshi; Šebera, Jakub; Kondo, Jiro; Oda, Shuji; Komuro, Tomoyuki; Kawamura, Takuya; Dairaku, Takenori; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Burda, Jaroslav V.; Kojima, Chojiro; Sychrovský, Vladimír; Tanaka, Yoshiyuki

    2014-01-01

    We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem HgII-mediated T–T base pairs (thymine–HgII–thymine, T–HgII–T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of ‘NATURAL’ bases. The T–HgII–T base pairs whose chemical structure was determined with the 15N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson–Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy (ΔS) for the T–HgII–T base pair formation. The positive ΔS value arises owing to the HgII dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards HgII and revealed arrangement of T–HgII–T base pairs in metallo-DNA. PMID:24371287

  5. Lewis pair polymerization by classical and frustrated Lewis pairs: acid, base and monomer scope and polymerization mechanism.

    PubMed

    Zhang, Yuetao; Miyake, Garret M; John, Mallory G; Falivene, Laura; Caporaso, Lucia; Cavallo, Luigi; Chen, Eugene Y-X

    2012-08-14

    Classical and frustrated Lewis pairs (LPs) of the strong Lewis acid (LA) Al(C(6)F(5))(3) with several Lewis base (LB) classes have been found to exhibit exceptional activity in the Lewis pair polymerization (LPP) of conjugated polar alkenes such as methyl methacrylate (MMA) as well as renewable α-methylene-γ-butyrolactone (MBL) and γ-methyl-α-methylene-γ-butyrolactone (γ-MMBL), leading to high molecular weight polymers, often with narrow molecular weight distributions. This study has investigated a large number of LPs, consisting of 11 LAs as well as 10 achiral and 4 chiral LBs, for LPP of 12 monomers of several different types. Although some more common LAs can also be utilized for LPP, Al(C(6)F(5))(3)-based LPs are far more active and effective than other LA-based LPs. On the other hand, several classes of LBs, when paired with Al(C(6)F(5))(3), can render highly active and effective LPP of MMA and γ-MMBL; such LBs include phosphines (e.g., P(t)Bu(3)), chiral chelating diphosphines, N-heterocyclic carbenes (NHCs), and phosphazene superbases (e.g., P(4)-(t)Bu). The P(4)-(t)Bu/Al(C(6)F(5))(3) pair exhibits the highest activity of the LP series, with a remarkably high turn-over frequency of 9.6 × 10(4) h(-1) (0.125 mol% catalyst, 100% MMA conversion in 30 s, M(n) = 2.12 × 10(5) g mol(-1), PDI = 1.34). The polymers produced by LPs at RT are typically atactic (P(γ)MMBL with ∼47% mr) or syndio-rich (PMMA with ∼70-75% rr), but highly syndiotactic PMMA with rr ∼91% can be produced by chiral or achiral LPs at -78 °C. Mechanistic studies have identified and structurally characterized zwitterionic phosphonium and imidazolium enolaluminates as the active species of the current LPP system, which are formed by the reaction of the monomer·Al(C(6)F(5))(3) adduct with P(t)Bu(3) and NHC bases, respectively. Kinetic studies have revealed that the MMA polymerization by the (t)Bu(3)P/Al(C(6)F(5))(3) pair is zero-order in monomer concentration after an initial

  6. Lewis pair polymerization by classical and frustrated Lewis pairs: acid, base and monomer scope and polymerization mechanism.

    PubMed

    Zhang, Yuetao; Miyake, Garret M; John, Mallory G; Falivene, Laura; Caporaso, Lucia; Cavallo, Luigi; Chen, Eugene Y-X

    2012-08-14

    Classical and frustrated Lewis pairs (LPs) of the strong Lewis acid (LA) Al(C(6)F(5))(3) with several Lewis base (LB) classes have been found to exhibit exceptional activity in the Lewis pair polymerization (LPP) of conjugated polar alkenes such as methyl methacrylate (MMA) as well as renewable α-methylene-γ-butyrolactone (MBL) and γ-methyl-α-methylene-γ-butyrolactone (γ-MMBL), leading to high molecular weight polymers, often with narrow molecular weight distributions. This study has investigated a large number of LPs, consisting of 11 LAs as well as 10 achiral and 4 chiral LBs, for LPP of 12 monomers of several different types. Although some more common LAs can also be utilized for LPP, Al(C(6)F(5))(3)-based LPs are far more active and effective than other LA-based LPs. On the other hand, several classes of LBs, when paired with Al(C(6)F(5))(3), can render highly active and effective LPP of MMA and γ-MMBL; such LBs include phosphines (e.g., P(t)Bu(3)), chiral chelating diphosphines, N-heterocyclic carbenes (NHCs), and phosphazene superbases (e.g., P(4)-(t)Bu). The P(4)-(t)Bu/Al(C(6)F(5))(3) pair exhibits the highest activity of the LP series, with a remarkably high turn-over frequency of 9.6 × 10(4) h(-1) (0.125 mol% catalyst, 100% MMA conversion in 30 s, M(n) = 2.12 × 10(5) g mol(-1), PDI = 1.34). The polymers produced by LPs at RT are typically atactic (P(γ)MMBL with ∼47% mr) or syndio-rich (PMMA with ∼70-75% rr), but highly syndiotactic PMMA with rr ∼91% can be produced by chiral or achiral LPs at -78 °C. Mechanistic studies have identified and structurally characterized zwitterionic phosphonium and imidazolium enolaluminates as the active species of the current LPP system, which are formed by the reaction of the monomer·Al(C(6)F(5))(3) adduct with P(t)Bu(3) and NHC bases, respectively. Kinetic studies have revealed that the MMA polymerization by the (t)Bu(3)P/Al(C(6)F(5))(3) pair is zero-order in monomer concentration after an initial

  7. A subcarrier-pair based resource allocation scheme using proportional fairness for cooperative OFDM-based cognitive radio networks.

    PubMed

    Ma, Yongtao; Zhou, Liuji; Liu, Kaihua

    2013-08-09

    The paper presents a joint subcarrier-pair based resource allocation algorithm in order to improve the efficiency and fairness of cooperative multiuser orthogonal frequency division multiplexing (MU-OFDM) cognitive radio (CR) systems. A communication model where one source node communicates with one destination node assisted by one half-duplex decode-and-forward (DF) relay is considered in the paper. An interference-limited environment is considered, with the constraint of transmitted sum-power over all channels and aggregate average interference towards multiple primary users (PUs). The proposed resource allocation algorithm is capable of maximizing both the system transmission efficiency and fairness among secondary users (SUs). Besides, the proposed algorithm can also keep the interference introduced to the PU bands below a threshold. A proportional fairness constraint is used to assure that each SU can achieve a required data rate, with quality of service guarantees. Moreover, we extend the analysis to the scenario where each cooperative SU has no channel state information (CSI) about non-adjacent links. We analyzed the throughput and fairness tradeoff in CR system. A detailed analysis of the performance of the proposed algorithm is presented with the simulation results.

  8. Pairing state with a time-reversal symmetry breaking in FeAs-based superconductors.

    PubMed

    Lee, Wei-Cheng; Zhang, Shou-Cheng; Wu, Congjun

    2009-05-29

    We investigate the competition between the extended s+/--wave and dx2-y2-wave pairing order parameters in the iron-based superconductors. Because of the frustrating pairing interactions among the electron and the hole Fermi pockets, a time-reversal symmetry breaking s+id pairing state could be favored. We analyze this pairing state within the Ginzburg-Landau theory and explore the experimental consequences. In such a state, spatial inhomogeneity induces a supercurrent near a nonmagnetic impurity and the corners of a square sample. The resonance mode between the s+/-- and dx2-y2-wave order parameters can be detected through the B1g Raman spectroscopy.

  9. Pairing state with a time-reversal symmetry breaking in FeAs-based superconductors

    SciTech Connect

    Lee, Wei-Sheng

    2010-05-26

    We investigate the competition between the extended s{+-} wave and dx2-y2 -wave pairing order parameters in the iron-based superconductors. Because of the frustrating pairing interactions among the electron and the hole fermi pockets, a time-reversal symmetry breaking s + id pairing state could be favored. We analyze this pairing state within the Ginzburg-Landau theory, and explore the experimental consequences. In such a state, spatial inhomogeneity induces supercurrent near a non-magnetic impurity and the corners of a square sample. The resonance mode between the s{+-} and dx2?y2 -wave order parameters can be detected through the B1g-Raman spectroscopy.

  10. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues

    SciTech Connect

    Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri; Sumpter, Bobby G; Fuentes-Cabrera, Miguel A; Vazquez-Mayagoitia, Alvaro

    2010-01-01

    Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.

  11. [Fourier Transform Spectrometer Based on Rotating Parallel-Mirror-Pair].

    PubMed

    Zhao, Bao-wei; Xiangli, Bin; Cai, Qi-sheng; Lü, Qun-bo; Zhou, Jin-song

    2015-11-01

    In the temporally-modulated Fourier transform spectroscopy, the translational moving mirror is difficult to drive accurately, causing tilt and shear problems. While, a rotational moving mirror can solve these problems. A rotary Fourier transform spectrometer is recommanded in this paper. Its principle is analyzed and the optical path difference is deduced. Also, the constrains for engineering realization are presented. This spectrometer consists of one beamsplitter, two fixed mirrors, one rotating parallel mirror pair, a collimating lens, a collecting lens, and one detector. From it's principle, this spectrometer show a simple structure, and it is assembled and adjustmented easily because the two split light are interfered with each other after reflected through the same plane mirror; By calculating the expression of it's optical path difference, the spectrometer is easy to realize large optical path difference, meaning high spectral resolution; Through analyzing it's engineering design constraints and computer simulation, it is known that the spectrometer should get the high resolution sample by high-speed spinning motor, so it is easy to achieve precise motion control, good stability, fast measurement speed.

  12. A cohesin-based structural platform supporting homologous chromosome pairing in meiosis.

    PubMed

    Ding, Da-Qiao; Haraguchi, Tokuko; Hiraoka, Yasushi

    2016-08-01

    The pairing and recombination of homologous chromosomes during the meiotic prophase is necessary for the accurate segregation of chromosomes in meiosis. However, the mechanism by which homologous chromosomes achieve this pairing has remained an open question. Meiotic cohesins have been shown to affect chromatin compaction; however, the impact of meiotic cohesins on homologous pairing and the fine structures of cohesion-based chromatin remain to be determined. A recent report using live-cell imaging and super-resolution microscopy demonstrated that the lack of meiotic cohesins alters the chromosome axis structures and impairs the pairing of homologous chromosomes. These results suggest that meiotic cohesin-based chromosome axis structures are crucial for the pairing of homologous chromosomes.

  13. Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs

    PubMed Central

    Wright, A.; Krousel-Wood, M.; Thomas, E. J.; McCoy, J. A.; Sittig, D. F.

    2015-01-01

    Summary Background Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. Objective We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. Methods We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. Results The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. Conclusions We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes. PMID:26171079

  14. An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules

    PubMed Central

    Kimoto, Michiko; Kawai, Rie; Mitsui, Tsuneo; Yokoyama, Shigeyuki; Hirao, Ichiro

    2009-01-01

    Toward the expansion of the genetic alphabet, we present an unnatural base pair system for efficient PCR amplification, enabling the site-specific incorporation of extra functional components into DNA. This system can be applied to conventional PCR protocols employing DNA templates containing unnatural bases, natural and unnatural base triphosphates, and a 3′→5′ exonuclease-proficient DNA polymerase. For highly faithful and efficient PCR amplification involving the unnatural base pairing, we identified the natural-base sequences surrounding the unnatural bases in DNA templates by an in vitro selection technique, using a DNA library containing the unnatural base. The system facilitates the site-specific incorporation of a variety of modified unnatural bases, linked with functional groups of interest, into amplified DNA. DNA fragments (0.15 amol) containing the unnatural base pair can be amplified 107-fold by 30 cycles of PCR, with <1% total mutation rate of the unnatural base pair site. Using the system, we demonstrated efficient PCR amplification and functionalization of DNA fragments for the extremely sensitive detection of zeptomol-scale target DNA molecules from mixtures with excess amounts (pmol scale) of foreign DNA species. This unnatural base pair system will be applicable to a wide range of DNA/RNA-based technologies. PMID:19073696

  15. Detection of base pair mismatches in duplex DNA and RNA oligonucleotides using electrospray mass spectrometry

    NASA Astrophysics Data System (ADS)

    Griffey, Richard H.; Greig, Michael J.

    1997-05-01

    The identify and location of base pair mismatches in non- covalent DNA:RNA duplexes are established using MS and MS-MS on a quadruple ion trap with electrospray ionization (ESI). MS-MS experiments on a 14mer duplex (D) with a single C:A base pair mismatch using lower activation energy results in selective cleavage of the mismatched A nucleobase, even in the presence of the wild-type duplex. The location of the mismatch base pair can be discerned via presence of the wild-type duplex. The location of the mismatch base pair can be discerned via selection of the (D-5H)5- ion and fragmentation of the backbone at that location in a n additional MS-MS experiment. Selective fragmentation is observed for C in a C-C mismatched base pair, which is very difficult to detect using chemical cleavage or E. coli mismatch binding protein. In an RNA:DNA duplex with a single base pair mismatch, the DNA base is removed without fragmentation of the RNA strand, greatly simplifying the interpretation of the resulting MS spectrum. A method is presented for detecting two DNA strands, for example a point mutation which generates an oncogenic phenotype, and the wild-type message. The results suggest that ESI-MS-MS may provide a rapid and selective method to identify and locate genetic mutations without the need for chemical degradation or protein binding followed by gel electrophoresis.

  16. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.

    PubMed

    Chawla, Mohit; Oliva, Romina; Bujnicki, Janusz M; Cavallo, Luigi

    2015-08-18

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. 'modified base pairs'. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson-Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in. PMID:26117545

  17. Fluorescent Protein Based FRET Pairs with Improved Dynamic Range for Fluorescence Lifetime Measurements.

    PubMed

    George Abraham, Bobin; Sarkisyan, Karen S; Mishin, Alexander S; Santala, Ville; Tkachenko, Nikolai V; Karp, Matti

    2015-01-01

    Fluorescence Resonance Energy Transfer (FRET) using fluorescent protein variants is widely used to study biochemical processes in living cells. FRET detection by fluorescence lifetime measurements is the most direct and robust method to measure FRET. The traditional cyan-yellow fluorescent protein based FRET pairs are getting replaced by green-red fluorescent protein variants. The green-red pair enables excitation at a longer wavelength which reduces cellular autofluorescence and phototoxicity while monitoring FRET. Despite the advances in FRET based sensors, the low FRET efficiency and dynamic range still complicates their use in cell biology and high throughput screening. In this paper, we utilized the higher lifetime of NowGFP and screened red fluorescent protein variants to develop FRET pairs with high dynamic range and FRET efficiency. The FRET variations were analyzed by proteolytic activity and detected by steady-state and time-resolved measurements. Based on the results, NowGFP-tdTomato and NowGFP-mRuby2 have shown high potentials as FRET pairs with large fluorescence lifetime dynamic range. The in vitro measurements revealed that the NowGFP-tdTomato has the highest Förster radius for any fluorescent protein based FRET pairs yet used in biological studies. The developed FRET pairs will be useful for designing FRET based sensors and studies employing Fluorescence Lifetime Imaging Microscopy (FLIM). PMID:26237400

  18. Fermiology, orbital order, orbital fluctuations, and Cooper pairing in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Yang, Fan; Wang, Fa; Lee, Dung-Hai

    2013-09-01

    We address two important issues that arise in recent studies of iron-based superconductivity. (1) Why are the Tc of AxFe2-ySe2 (A=K, Rb, Cs) and the single unit cell FeSe on SrTiO3 so high despite both only having electron pockets? (2) What (if any) are the effects of orbital order and orbital fluctuation on the Cooper pairing. Our main conclusions are the following: (1) removing hole pockets releases frustration of Cooper pairing from their band vorticity, therefore can enhance Tc, and (2) orbital fluctuation has negligible effect on Cooper pairing.

  19. Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing.

    PubMed

    Tatsumi, Kaori; Nishimura, Osamu; Itomi, Kazu; Tanegashima, Chiharu; Kuraku, Shigehiro

    2015-05-01

    In de novo genome sequencing, mate-pair reads are crucial for scaffolding assembled contigs. However, preparation of mate-pair libraries is not a trivial task, even when using one of the latest approaches, the Nextera Mate Pair Sample Prep Kit from Illumina. To reduce cost and enhance library yield and fidelity when using this kit, we have modified the manufacturer's protocol based on (i) variable tagmentation conditions, (ii) intensive DNA shearing to decrease library insert length, and (iii) sequencing on an Illumina HiSeq with >150 cycles. Finally, we provide additional suggestions for further improvement in the application of this kit.

  20. Multi-hop teleportation based on W state and EPR pairs

    NASA Astrophysics Data System (ADS)

    Hai-Tao, Zhan; Xu-Tao, Yu; Pei-Ying, Xiong; Zai-Chen, Zhang

    2016-05-01

    Multi-hop teleportation has significant value due to long-distance delivery of quantum information. Many studies about multi-hop teleportation are based on Bell pairs, partially entangled pairs or W state. The possibility of multi-hop teleportation constituted by partially entangled pairs relates to the number of nodes. The possibility of multi-hop teleportation constituted by double W states is after n-hop teleportation. In this paper, a multi-hop teleportation scheme based on W state and EPR pairs is presented and proved. The successful possibility of quantum information transmitted hop by hop through intermediate nodes is deduced. The possibility of successful transmission is after n-hop teleportation. Project supported by the National Natural Science Foundation of China (Grant No. 61571105), the Prospective Future Network Project of Jiangsu Province, China (Grant No. BY2013095-1-18), and the Independent Project of State Key Laboratory of Millimeter Waves, China (Grant No. Z201504).

  1. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

    PubMed Central

    Chawla, Mohit; Oliva, Romina; Bujnicki, Janusz M.; Cavallo, Luigi

    2015-01-01

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in. PMID:26117545

  2. Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

    PubMed Central

    Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

    2014-01-01

    The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. PMID:24399194

  3. Discrete Frequency Entangled Photon Pair Generation Based on Silicon Micro-ring Cavities

    NASA Astrophysics Data System (ADS)

    Suo, Jing; Zhang, Wei; Dong, Shuai; Huang, Yidong; Peng, Jiangde

    2016-10-01

    In this paper, we propose and demonstrate a scheme to generate discrete frequency entangled photon pairs based on a silicon micro-ring resonator. The resonator is placed in a Sagnac fiber loop. Stimulated by two pump lights at two different resonance wavelengths of the resonator, photon pairs at another two resonance wavelengths are generated along two opposite directions in the fiber loop, by the nondegenerate spontaneous four wave mixing in the resonator. Their states are superposed and interfered at the output ports of the fiber loop to generate frequency entangled photon pairs. On the other hand, since the pump lights come from two continuous wave lasers, energy-time entanglement is an intrinsic property of the generated photon pairs. The entanglements on frequency and energy-time are demonstrated experimentally by the experiments of spatial quantum beating and Franson-type interference, respectively, showing that the silicon micro-ring resonators are ideal candidates to realize complex photonic quantum state generation.

  4. Generation of arbitrary vector fields based on a pair of orthogonal elliptically polarized base vectors.

    PubMed

    Xu, Danfeng; Gu, Bing; Rui, Guanghao; Zhan, Qiwen; Cui, Yiping

    2016-02-22

    We present an arbitrary vector field with hybrid polarization based on the combination of a pair of orthogonal elliptically polarized base vectors on the Poincaré sphere. It is shown that the created vector field is only dependent on the latitude angle 2χ but is independent on the longitude angle 2ψ on the Poincaré sphere. By adjusting the latitude angle 2χ, which is related to two identical waveplates in a common path interferometric arrangement, one could obtain arbitrary type of vector fields. Experimentally, we demonstrate the generation of such kind of vector fields and confirm the distribution of state of polarization by the measurement of Stokes parameters. Besides, we investigate the tight focusing properties of these vector fields. It is found that the additional degree of freedom 2χ provided by arbitrary vector field with hybrid polarization allows one to control the spatial structure of polarization and to engineer the focusing field. PMID:26907066

  5. VAMMPIRE: a matched molecular pairs database for structure-based drug design and optimization.

    PubMed

    Weber, Julia; Achenbach, Janosch; Moser, Daniel; Proschak, Ewgenij

    2013-06-27

    Structure-based optimization to improve the affinity of a lead compound is an established approach in drug discovery. Knowledge-based databases holding molecular replacements can be supportive in the optimization process. We introduce a strategy to relate the substitution effect within matched molecular pairs (MMPs) to the atom environment within the cocrystallized protein-ligand complex. Virtually Aligned Matched Molecular Pairs Including Receptor Environment (VAMMPIRE) database and the supplementary web interface ( http://vammpire.pharmchem.uni-frankfurt.de ) provide valuable information for structure-based lead optimization.

  6. Comparison of Sedimentary Processes on Adjacent Passive and Active Continental Margins Offshore of Southwest Taiwan Based on Echo Character Studies

    NASA Astrophysics Data System (ADS)

    Liu, C.; Chiu, J.

    2008-12-01

    Echo character recorded on Chirp sub-bottom sonar data from offshore area of southwest Taiwan were analyzed to examine and compare the sedimentary processes of adjacent passive and active continental margin settings. Seafloor echoes in the study area are classified into four types: (1) distinct echoes, (2) indistinct echoes, (3) hyperbolic echoes, and (4) irregular echoes. Based on the mapped distribution of the echo types, the sedimentary processes offshore of southwest Taiwan are different in the two tectonic settings. On the passive South China Sea margin, slope failure is the main process on the upper continental slope, whereas turbidite deposits accumulate in the lower continental slope. In contrast, the submarine Taiwan orogenic wedge is characterized by fill-and-spill processes in the intraslope basins of the upper slope, and mass-transport deposits are observed in the canyons and on the lower Kaoping slope. This difference is largely caused by the huge influx of terrigenous sediments into the submarine Taiwan orogenic wedge province compared to the passive South China Sea continental margin. In the passive South China Sea margin, loading and movement of the Taiwan orogenic wedge has had significant effect on the seafloor morphology, and triggered retrogressive failures. Gas hydrate dissociation may have enhanced the slope failure processes at some locations.

  7. Detour matrix-based adjacent path eccentric distance sum indices for QSAR/QSPR. Part I: development and evaluation.

    PubMed

    Singh, Monika; Bharatam, P V; Madan, A K

    2014-01-01

    In the present study, three detour matrix-based topological indices (TIs) termed as adjacent path eccentric distance sum indices 1-3 (denoted by (A)ξ(1)(PDS), (A)ξ(2)(PDS) and (A)ξ(3)(PDS)) as well as their topochemical versions (denoted by (A)ξ(1c)(PDS), (A)ξ(2c)(PDS) and (A)ξ(3c)(PDS)) have been conceptualised. Values of the proposed TIs were computed for all possible cyclic and acyclic structures containing three, four, five vertices using an in-house computer programme. Proposed TIs were evaluated for discriminating power, degeneracy, intercorrelation and sensitivity towards branching as well relative position of substituent(s) in cyclic structures. Mathematical properties of one of the proposed TIs were also studied. Exceptionally high discriminating power, high sensitivity towards branching as well as relative position(s) of substituent(s) in cyclic structures and negligible degeneracy offer proposed indices a vast potential for use in characterisation of structures, similarity/dissimilarity studies, lead identification and optimisation, combinatorial library design and quantitative structure-activity/property/toxicity/pharmacokinetic relationship studies so as to facilitate drug design.

  8. PAIRS, The GIS-Based Incident Response System for Pennsylvania, and NASA

    NASA Technical Reports Server (NTRS)

    Conrad, Eric; Arbegast, Daniel; Maynard, Nancy; Vicente, Gilberto

    2003-01-01

    Over the past several years the Pennsylvania Departments of Environmental Protection (DEP), Health (DOH), and Agriculture (PDA) built the GIs-based Pennsylvania West Nile Surveillance System. That system has become a model for collecting data that has a field component, laboratory component, reporting and mapping component, and a public information component. Given the success of the West Nile Virus System and the events of September 11, 2001, DEP then embarked on the development of the Pennsylvania Incident Response System, or PAIRS. PAIRS is an effective GIs-based approach to providing a system for response to incidents of any kind, including terrorism because it is building upon the existing experience, infrastructure and databases that were successfully developed to respond to the West Nile Virus by DEP, DOH, and PDA. The proposed system can be described as one that supports data acquisition, laboratory forensics, decision making/response, and communications. Decision makers will have tools to view and analyze data from various sources and, at the same time, to communicate with the large numbers of people responding to the same incident. Recent collaborations with NASA partners are creating mechanisms for the PAIRS system to incorporate space-based and other remote sensing geophysical parameters relevant to public health assessment and management, such as surface temperatures, precipitation, land cover/land use change, and humidity. This presentation will describe the PAIRS system and outline the Pennsylvania-NASA collaboration for integration of space-based data into the PAIRS system.

  9. Discrimination of Single Base Pair Differences Among Individual DNA Molecules Using a Nanopore

    NASA Technical Reports Server (NTRS)

    Vercoutere, Wenonah; DeGuzman, Veronica

    2003-01-01

    The protein toxin alpha-hemolysin form nanometer scale channels across lipid membranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, base pair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, in current. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.

  10. Fermi surface nesting induced strong pairing in iron-based superconductors

    PubMed Central

    Terashima, K.; Sekiba, Y.; Bowen, J. H.; Nakayama, K.; Kawahara, T.; Sato, T.; Richard, P.; Xu, Y.-M.; Li, L. J.; Cao, G. H.; Xu, Z.-A.; Ding, H.; Takahashi, T.

    2009-01-01

    The discovery of high-temperature superconductivity in iron pnictides raised the possibility of an unconventional superconducting mechanism in multiband materials. The observation of Fermi-surface (FS)-dependent nodeless superconducting gaps suggested that inter-FS interactions may play a crucial role in superconducting pairing. In the optimally hole-doped Ba0.6K0.4Fe2As2, the pairing strength is enhanced simultaneously (2Δ/Tc≈7) on the nearly nested FS pockets, i.e., the inner hole-like (α) FS and the 2 hybridized electron-like FSs, whereas the pairing remains weak (2Δ/Tc≈3.6) in the poorly nested outer hole-like (β) FS. Here, we report that in the electron-doped BaFe1.85Co0.15As2, the FS nesting condition switches from the α to the β FS due to the opposite size changes for hole- and electron-like FSs upon electron doping. The strong pairing strength (2Δ/Tc≈6) is also found to switch to the nested β FS, indicating an intimate connection between FS nesting and superconducting pairing, and strongly supporting the inter-FS pairing mechanism in the iron-based superconductors. PMID:19359490

  11. [Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

    PubMed

    Petrenko, Y M

    2015-01-01

    Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

  12. Single-molecule derivation of salt dependent base-pair free energies in DNA.

    PubMed

    Huguet, Josep M; Bizarro, Cristiano V; Forns, Núria; Smith, Steven B; Bustamante, Carlos; Ritort, Felix

    2010-08-31

    Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol(-1) precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our unique energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies, and entropies in conditions not accessible by bulk methodologies. PMID:20716688

  13. Solution structure of a DNA double helix with consecutive metal-mediated base pairs.

    PubMed

    Johannsen, Silke; Megger, Nicole; Böhme, Dominik; Sigel, Roland K O; Müller, Jens

    2010-03-01

    Metal-mediated base pairs represent a powerful tool for the site-specific functionalization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artificial nucleotides forming the loop. In the presence of Ag(i) ions, a duplex comprising three imidazole-Ag(+)-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from ¹J(¹⁵N,¹⁰⁷/¹⁰⁹Ag) couplings upon incorporation of ¹⁵N-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artificial bases. This work represents the first structural characterization of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs. PMID:21124482

  14. A Bayesian-based Method for Particle Track Identification in Low-energy Pair-creation Telescopes

    SciTech Connect

    Zoglauer, Andreas; Andritschke, Robert; Kanbach, Gottfried; Boggs, Steven E.

    2007-07-12

    A critical step during the data analysis of pair creation telescopes is the correct identification of the electron and positron tracks. For MEGA, an electron-tracking Compton and pair telescope optimized for energies up to 50 MeV, we describe a low-energy pair event reconstruction approach partly based on Bayesian statistics.

  15. Concealed d-wave pairs in the s± condensate of iron-based superconductors.

    PubMed

    Ong, Tzen; Coleman, Piers; Schmalian, Jörg

    2016-05-17

    A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave ([Formula: see text]) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. Here, we propose a new class of [Formula: see text] state containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave ([Formula: see text]) motion of the pairs with the internal angular momenta [Formula: see text] of the iron orbitals to make a singlet ([Formula: see text]), an [Formula: see text] superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba1-x KXFe2As2 as a reconfiguration of the orbital and internal angular momentum into a high spin ([Formula: see text]) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. The formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy. PMID:27140626

  16. Genome filtering using methylation-sensitive restriction enzymes with six-base pair recognition sites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large fraction of repetitive DNA in many plant genomes has complicated all aspects of DNA sequencing and assembly, and thus techniques that enrich for genes and low-copy sequences have been employed to isolate gene space. Methyl sensitive restriction enzymes with six base pair recognition sites...

  17. Free energy analysis and mechanism of base pair stacking in nicked DNA

    PubMed Central

    Häse, Florian; Zacharias, Martin

    2016-01-01

    The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner. PMID:27407106

  18. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes

    PubMed Central

    Léon, J. Christian; Sinha, Indranil; Müller, Jens

    2016-01-01

    The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase. PMID:27089326

  19. Free energy analysis and mechanism of base pair stacking in nicked DNA.

    PubMed

    Häse, Florian; Zacharias, Martin

    2016-09-01

    The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner. PMID:27407106

  20. Seismic hazard and seismic risk assessment based on the unified scaling law for earthquakes: Himalayas and adjacent regions

    NASA Astrophysics Data System (ADS)

    Nekrasova, A. K.; Kossobokov, V. G.; Parvez, I. A.

    2015-03-01

    magnitudes which, according to USLE, corresponded to the probability of exceedance 1% and 10% during 50 years or, if the reliable estimate is absent, the maximal magnitudes reported during the instrumental period. As a result, the seismic hazard maps for the Himalayas and the adjacent regions in terms of standard seismic zoning were constructed. Based on these calculations, in order to exemplify the method, we present a series of seismic risk maps taking into account the population density prone to seismic hazard and the dependence of the risk on the vulnerability as a function of population density.

  1. Tuning Locality of Pair Coherence in Graphene-based Andreev Interferometers

    PubMed Central

    Kim, Minsoo; Jeong, Dongchan; Lee, Gil-Ho; Shin, Yun-Sok; Lee, Hyun-Woo; Lee, Hu-Jong

    2015-01-01

    We report on gate-tuned locality of superconductivity-induced phase-coherent magnetoconductance oscillations in a graphene-based Andreev interferometer, consisting of a T-shaped graphene bar in contact with a superconducting Al loop. The conductance oscillations arose from the flux change through the superconducting Al loop, with gate-dependent Fraunhofer-type modulation of the envelope. We confirm a transitional change in the character of the pair coherence, between local and nonlocal, in the same device as the effective length-to-width ratio of the device was modulated by tuning the pair-coherence length ξT in the graphene layer. PMID:25737106

  2. Pair correlation functions of FeAs-based superconductors: Quantum Monte Carlo study

    NASA Astrophysics Data System (ADS)

    Kashurnikov, V. A.; Krasavin, A. V.

    2015-01-01

    The new generalized quantum continuous time world line Monte Carlo algorithm was developed to calculate pair correlation functions for two-dimensional FeAs-clusters modeling of iron-based superconductors within the framework of the two-orbital model. The analysis of pair correlations depending on the cluster size, temperature, interaction, and the type of symmetry of the order parameter is carried out. The data obtained for clusters with sizes up to 1 0x1 0 FeAs-cells favor the possibility of an effective charge carrier's attraction that is corresponding the A1g-symmetry, at some parameters of interaction.

  3. Identity-based authenticated key exchange protocols from the Tate pairing

    NASA Astrophysics Data System (ADS)

    Shen, Jun; Jin, Hong; Yang, Zhiyong; Cui, Xiang

    2011-12-01

    Key agreement protocols are designed to establish a session keys between two or multiple entities oven an insecure network and the session key is used to assure confidentiality thought encryption. With the advantages of identity-based (ID-based) cryptography, there have been many ID-based key agreement protocols proposed. However, most of them are based on Weil pairing, which is more cost of computation compared with Tate paring. In this paper, we propose a newly ID-based key agreement protocol from the Tate pairing. Compared with previous protocols, the new protocol minimizes the cost of computation with no extra message exchange time. In addition, the proposed protocol provides known key security, no key control, no key-compromise impersonation and perfect forward secrecy.

  4. The conformational flexibility of nucleic acid bases paired in gas phase: A Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Xiao, Shiyan; Liang, Haojun

    2012-05-01

    The flexibilities of pyrimidine and imidazole rings in the paired nucleobases are investigated using Car-Parrinello molecular dynamics simulation in gas phase. The pairing influence on the stiffness of rings is analyzed based on the molecular structure of the nucleobases and constraints caused by pairing. We prove that the flexibilities of pyrimidine rings in isolated state have subtle correlation with the degree of aromaticity of the rings. The pairings in nucleic base pairs cause the rings to be more rigid for G, T, and U but more flexible for A and the same for C.

  5. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Rodgers, M. T.

    2015-08-01

    Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

  6. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m(5)dCyd: Implications for the Stability of DNA i-Motif Conformations.

    PubMed

    Yang, Bo; Rodgers, M T

    2015-08-01

    Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m(5)dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m(5)dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m(5)dCyd)H(+)(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

  7. Binding of T and T analogs to CG base pairs in antiparallel triplexes.

    PubMed

    Durland, R H; Rao, T S; Revankar, G R; Tinsley, J H; Myrick, M A; Seth, D M; Rayford, J; Singh, P; Jayaraman, K

    1994-08-11

    The goal of this study was to address antiparallel triplex formation at duplex targets that do not conform to a strict oligopurine.oligopyrimidine motif. We focused on the ability of natural bases and base analogs incorporated into oligonucleotide third strands to bind to so-called CG inversions. These are sites where a cytosine base is present in an otherwise purine-rich strand of a duplex target. Using a 26-base-triplet test system, we found that of the standard bases, only thymine (T) shows substantial binding to CG inversions. This is quantitatively similar to the report of Beal and Dervan [Science (1991), 251, 1360-1363]. Binding to CG inversions was only slightly weaker than binding to AT base pairs. Binding of T to CG inversions was also evaluated in two other sequences, with qualitatively similar results. Six different analogs of thymine were also tested for binding to CG inversions and AT base pairs. Significant changes in affinity were observed. In particular, 5-fluoro-2'-deoxyuridine was found to increase affinity for CG inversions as well as for AT base pairs. Studies with oligonucleotides containing pyridin-2-one or pyridin-4-one suggest that thymine O4 plays a critical role in the T.CG interaction. Possible models to account for these observations are discussed. PMID:8065940

  8. Electron pairing in the presence of incipient bands in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Chen, Xiao; Maiti, S.; Linscheid, A.; Hirschfeld, P. J.

    2015-12-01

    Recent experiments on certain Fe-based superconductors have hinted at a role for paired electrons in "incipient" bands that are close to, but do not cross, the Fermi level. Related theoretical works disagree on whether or not strong-coupling superconductivity is required to explain such effects, and whether a critical interaction strength exists. In this work, we consider various versions of the model problem of pairing of electrons in the presence of an incipient band, within a simple multiband weak-coupling BCS approximation. We categorize the problem into two cases: case (i), where superconductivity arises from the "incipient band pairing" alone, and case (ii), where it is induced on an incipient band by pairing due to Fermi-surface-based interactions. Negative conclusions regarding the importance of incipient bands have been drawn so far largely based on case (i), but we show explicitly that models under case (ii) are qualitatively different, and can explain the nonexponential suppression of Tc, as well as robust large gaps on an incipient band. In the latter situation, large gaps on the incipient band do not require a critical interaction strength. We also model the interplay between phonon and spin fluctuation driven superconductivity and describe situations in which they can enhance each other rather than compete. Finally, we discuss the effect of the dimensionality of the incipient band on our results. We argue that pairing on incipient bands may be significant and important in several Fe-based materials, including LiFeAs, FeSe intercalates, and FeSe monolayers on strontium titanate, and indeed may contribute to high critical temperatures in some cases.

  9. Acid-Base Pairs in Lewis Acidic Zeolites Promote Direct Aldol Reactions by Soft Enolization.

    PubMed

    Lewis, Jennifer D; Van de Vyver, Stijn; Román-Leshkov, Yuriy

    2015-08-17

    Hf-, Sn-, and Zr-Beta zeolites catalyze the cross-aldol condensation of aromatic aldehydes with acetone under mild reaction conditions with near quantitative yields. NMR studies with isotopically labeled molecules confirm that acid-base pairs in the Si-O-M framework ensemble promote soft enolization through α-proton abstraction. The Lewis acidic zeolites maintain activity in the presence of water and, unlike traditional base catalysts, in acidic solutions.

  10. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

    PubMed Central

    Hudson, Graham A.; Bloomingdale, Richard J.; Znosko, Brent M.

    2013-01-01

    Pseudouridine (Ψ) is the most common noncanonical nucleotide present in naturally occurring RNA and serves a variety of roles in the cell, typically appearing where structural stability is crucial to function. Ψ residues are isomerized from native uridine residues by a class of highly conserved enzymes known as pseudouridine synthases. In order to quantify the thermodynamic impact of pseudouridylation on U-A base pairs, 24 oligoribonucleotides, 16 internal and eight terminal Ψ-A oligoribonucleotides, were thermodynamically characterized via optical melting experiments. The thermodynamic parameters derived from two-state fits were used to generate linearly independent parameters for use in secondary structure prediction algorithms using the nearest-neighbor model. On average, internally pseudouridylated duplexes were 1.7 kcal/mol more stable than their U-A counterparts, and terminally pseudouridylated duplexes were 1.0 kcal/mol more stable than their U-A equivalents. Due to the fact that Ψ-A pairs maintain the same Watson-Crick hydrogen bonding capabilities as the parent U-A pair in A-form RNA, the difference in stability due to pseudouridylation was attributed to two possible sources: the novel hydrogen bonding capabilities of the newly relocated imino group as well as the novel stacking interactions afforded by the electronic configuration of the Ψ residue. The newly derived nearest-neighbor parameters for Ψ-A base pairs may be used in conjunction with other nearest-neighbor parameters for accurately predicting the most likely secondary structure of A-form RNA containing Ψ-A base pairs. PMID:24062573

  11. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides.

    PubMed

    Hudson, Graham A; Bloomingdale, Richard J; Znosko, Brent M

    2013-11-01

    Pseudouridine (Ψ) is the most common noncanonical nucleotide present in naturally occurring RNA and serves a variety of roles in the cell, typically appearing where structural stability is crucial to function. Ψ residues are isomerized from native uridine residues by a class of highly conserved enzymes known as pseudouridine synthases. In order to quantify the thermodynamic impact of pseudouridylation on U-A base pairs, 24 oligoribonucleotides, 16 internal and eight terminal Ψ-A oligoribonucleotides, were thermodynamically characterized via optical melting experiments. The thermodynamic parameters derived from two-state fits were used to generate linearly independent parameters for use in secondary structure prediction algorithms using the nearest-neighbor model. On average, internally pseudouridylated duplexes were 1.7 kcal/mol more stable than their U-A counterparts, and terminally pseudouridylated duplexes were 1.0 kcal/mol more stable than their U-A equivalents. Due to the fact that Ψ-A pairs maintain the same Watson-Crick hydrogen bonding capabilities as the parent U-A pair in A-form RNA, the difference in stability due to pseudouridylation was attributed to two possible sources: the novel hydrogen bonding capabilities of the newly relocated imino group as well as the novel stacking interactions afforded by the electronic configuration of the Ψ residue. The newly derived nearest-neighbor parameters for Ψ-A base pairs may be used in conjunction with other nearest-neighbor parameters for accurately predicting the most likely secondary structure of A-form RNA containing Ψ-A base pairs.

  12. Protein−DNA binding in the absence of specific base-pair recognition

    PubMed Central

    Afek, Ariel; Schipper, Joshua L.; Horton, John; Gordân, Raluca; Lukatsky, David B.

    2014-01-01

    Until now, it has been reasonably assumed that specific base-pair recognition is the only mechanism controlling the specificity of transcription factor (TF)−DNA binding. Contrary to this assumption, here we show that nonspecific DNA sequences possessing certain repeat symmetries, when present outside of specific TF binding sites (TFBSs), statistically control TF−DNA binding preferences. We used high-throughput protein−DNA binding assays to measure the binding levels and free energies of binding for several human TFs to tens of thousands of short DNA sequences with varying repeat symmetries. Based on statistical mechanics modeling, we identify a new protein−DNA binding mechanism induced by DNA sequence symmetry in the absence of specific base-pair recognition, and experimentally demonstrate that this mechanism indeed governs protein−DNA binding preferences. PMID:25313048

  13. DNA Aptamer Generation by Genetic Alphabet Expansion SELEX (ExSELEX) Using an Unnatural Base Pair System.

    PubMed

    Kimoto, Michiko; Matsunaga, Ken-ichiro; Hirao, Ichiro

    2016-01-01

    Genetic alphabet expansion of DNA using unnatural base pair systems is expected to provide a wide variety of novel tools and methods. Recent rapid progress in this area has enabled the creation of several types of unnatural base pairs that function as a third base pair in polymerase reactions. Presently, a major topic is whether the genetic alphabet expansion system actually increases nucleic acid functionalities. We recently applied our unnatural base pair system to in vitro selection (SELEX), using a DNA library containing four natural bases and an unnatural base, and succeeded in the generation of high-affinity DNA aptamers that specifically bind to target proteins. Only a few hydrophobic unnatural bases greatly augmented the affinity of the aptamers. Here, we describe a new approach (genetic alphabet Expansion SELEX, ExSELEX), using our hydrophobic unnatural base pair system for high affinity DNA aptamer generation. PMID:26552815

  14. Electronic transport in poly(CG) and poly(CT) DNA segments with diluted base pairing

    NASA Astrophysics Data System (ADS)

    de Moura, F. A. B. F.; Lyra, M. L.; Albuquerque, E. L.

    2008-02-01

    We present a model for describing electrical conductivity along poly(CG) and poly(CT) DNA segments with diluted base pairing within a tight-binding Hamiltonian approach. The base pairing is restricted to occurring at a fraction p of the cytosine (C) nucleotides at which a guanine (G) nucleotide is attached. We show that the Schrödinger equation can be mapped exactly onto that of the one-dimensional Anderson model with diluted disorder. Using a Green function formalism as well as exact diagonalization of the full one-dimensional Hamiltonian of finite segments, we compute the density of states, the wavefunction of all energy eigenstates and their corresponding localization lengths. We show that the effective disorder introduced by the diluted base pairing is much stronger in poly(CG) than in poly(CT) segments, with significant consequences for the electronic transport properties. The electronic wavepacket remains localized in the poly(CT) case, while it acquires a diffusive spread for the poly(CG)-based sequence.

  15. Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

    PubMed

    Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

    2012-11-01

    Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences. PMID:22766014

  16. Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

    PubMed

    Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

    2012-11-01

    Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences.

  17. An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.

    PubMed

    Dirks, Robert M; Pierce, Niles A

    2004-07-30

    Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure. PMID:15139042

  18. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

    PubMed Central

    Cafferty, Brian J.; Fialho, David M.; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V.

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life. PMID:27108699

  19. Hydrogen bonding: a channel for protons to transfer through acid-base pairs.

    PubMed

    Wu, Liang; Huang, Chuanhui; Woo, Jung-Je; Wu, Dan; Yun, Sung-Hyun; Seo, Seok-Jun; Xu, Tongwen; Moon, Seung-Hyeon

    2009-09-10

    Different from H(3)O(+) transport as in the vehicle mechanism, protons find another channel to transfer through the poorly hydrophilic interlayers in a hydrated multiphase membrane. This membrane was prepared from poly(phthalazinone ether sulfone kentone) (SPPESK) and H(+)-form perfluorosulfonic resin (FSP), and poorly hydrophilic electrostatically interacted acid-base pairs constitute the interlayer between two hydrophilic phases (FSP and SPPESK). By hydrogen bonds forming and breaking between acid-base pairs and water molecules, protons transport directly through these poorly hydrophilic zones. The multiphase membrane, due to this unique transfer mechanism, exhibits better electrochemical performances during fuel cell tests than those of pure FSP and Nafion-112 membranes: 0.09-0.12 S cm(-1) of proton conductivity at 25 degrees C and 990 mW cm(-2) of the maximum power density at a current density of 2600 mA cm(-2) and a cell voltage of 0.38 V.

  20. Hoogsteen base-pairing revisited: Resolving a role in normal biological processes and human diseases

    SciTech Connect

    Ghosal, Gargi; Muniyappa, K. . E-mail: kmbc@biochem.iisc.ernet.in

    2006-04-28

    For a long time since the discovery of an alternative type of hydrogen bonding between adenine and thymidine, termed Hoogsteen base-pairing, its biological role remained elusive. Recent experiments provide compelling evidence that Hoogsteen base pairs manifest in a gamut of nuclear processes encompassing gene expression, replication, recombination, and telomere length maintenance. An increasing number of proteins that have been shown to bind, unwind or cleave G-quadruplexes or triplexes with high specificity underscore their biological significance. In humans, the absence of these cellular factors or their dysfunction leads to a wide spectrum of genetic diseases including cancer, neurodegenerative syndromes, and a myriad of other disorders. Thus, development of clinically useful compounds that target G-quadruplexes or triplexes, and interfere with specific cellular processes, provides considerable promise for successful and improved treatment of human diseases.

  1. Electric-field induced mutation of DNA: a theoretical investigation of the GC base pair.

    PubMed

    Cerón-Carrasco, José P; Jacquemin, Denis

    2013-04-01

    It is known that intense external electric fields affect the proton transfer (PT) reactions in simple chemical systems, such as hydrated chlorhydric acid or formic acid dimer. Accordingly, electric fields might be used to modulate the PT reactions responsible for the spontaneous mutation mechanism in DNA. In this contribution, we investigate the effect of these fields on the tautomeric equilibria of the guanine-cytosine (GC) base pair in order to gain further insight into this hypothesis. This task is performed with both density functional theory (DFT) and second-order Møller-Plesset (MP2) approaches. Our results demonstrate that electric fields not only drastically alter the rate constants of PT but also tune the mechanism of the PT reactions in the GC base pair. PMID:23338206

  2. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water.

    PubMed

    Cafferty, Brian J; Fialho, David M; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life. PMID:27108699

  3. Electron pairing in the presence of incipient bands in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Linscheid, Andy; Chen, Xiao; Maiti, Saurabh; Hirschfeld, Peter

    Recent experiments on certain Fe-based superconductors (SC) have hinted at a role for paired electrons in ``incipient'' bands that are close to, but do not cross the Fermi level. Within a simple multiband weak-coupling BCS approximation, we categorize the problem into two cases: case(I) where SC arises from the incipient band pairing alone, and case(II) where it is induced on an incipient band by pairing due to Fermi-surface based interactions. Negative conclusions regarding the importance of incipient bands are largely based on case(I). However, we show explicitly that models under case(II) can explain the mild suppression of Tc, as well as robust large gaps on an incipient band. We also model the interplay between phonon and spin fluctuation (SF) driven SC and describe the bootstrap of electron-phonon SC by SF coupling the incipient and the regular bands. We argue that pairing on incipient bands may be important in several Fe-based materials, including LiFeAs, FeSe intercalates and FeSe monolayers on SrTiO3, and indeed may contribute to high Tc in some cases. In addition, we address the question whether this conclusion holds if the SF interaction is derived explicitly in the incipient band scenario and retardation effects are included on the level of the Eliashberg equations. SM was supported by NHMFL through NSF-DMR-1157490, AL and PJH were supported in part by DOE DE-FG02-05ER46236.

  4. Effects of halogen substitution on Watson-Crick base pairing: a possible mechanism for radiosensitivity.

    PubMed

    Heshmati, Emran; Abdolmaleki, Parviz; Mozdarani, Hossein; Sarvestani, Amir Sabet

    2009-09-01

    The halogen substituent effect on geometries and charge distributions of the A-T base pair derivatives was evaluated using density functional theory at B3LYP/6-31G* level. The results indicate that all of the substitutions affect geometries and charge distributions of the atoms contributing hydrogen bonds. These changes would be the reason of the radiosensitization of these compounds incorporating DNA. PMID:19643605

  5. Molecular dynamics simulation of DNA base-pair opening by sharp bending

    NASA Astrophysics Data System (ADS)

    Cong, Peiwen; Dai, Liang; van der Maarel, Johan R. C.; Yan, Jie

    2013-03-01

    Many biological processes require sharp bending of DNA. According to worm-like chain model, the bending energy dominates the free energy cost of those processes containing DNA loops shorter than 40 nm, such as DNA wrapping around histones, Lac repressor looping and virus DNA packaging. However, several recent experimental observations suggest that the WLC model s not applicable under tight bending conditions. In full atom molecular dynamics simulations, a double stranded, 20 base-pairs DNA fragment is forced to bend by an external spring. It is found that one or two AT-rich regions are disrupted for sufficiently small end-to-end distance. The disrupted DNA base-pairs separate and usually stack with the neighbouring base-pairs to form a defect. It is shown that these defects are more bendable than the bending rigidity of the duplex in the regular B-form. The simulation suggests a curvature dependent, non-harmonic bending elasticity of the DNA backbone is necessary to describe the DNA conformation under tight bending conditions.

  6. B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

    SciTech Connect

    Maehigashi, Tatsuya; Hsiao, Chiaolong; Woods, Kristen Kruger; Moulaei, Tinoush; Hud, Nicholas V.; Williams, Loren Dean

    2012-10-23

    Increasingly exact measurement of single crystal X-ray diffraction data offers detailed characterization of DNA conformation, hydration and electrostatics. However, instead of providing a more clear and unambiguous image of DNA, highly accurate diffraction data reveal polymorphism of the DNA atomic positions and conformation and hydration. Here we describe an accurate X-ray structure of B-DNA, painstakingly fit to a multistate model that contains multiple competing positions of most of the backbone and of entire base pairs. Two of ten base-pairs of CCAGGCCTGG are in multiple states distinguished primarily by differences in slide. Similarly, all the surrounding ions are seen to fractionally occupy discrete competing and overlapping sites. And finally, the vast majority of water molecules show strong evidence of multiple competing sites. Conventional resolution appears to give a false sense of homogeneity in conformation and interactions of DNA. In addition, conventional resolution yields an average structure that is not accurate, in that it is different from any of the multiple discrete structures observed at high resolution. Because base pair positional heterogeneity has not always been incorporated into model-building, even some high and ultrahigh-resolution structures of DNA do not indicate the full extent of conformational polymorphism.

  7. Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

    NASA Astrophysics Data System (ADS)

    Swasey, Steven M.; Gwinn, Elisabeth G.

    2016-04-01

    The thermal and chemical fragility of DNA nanomaterials assembled by Watson-Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag+, as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag+-DNA nanostructures. Our studies of Ag+-induced assembly of non-complementary DNA oligomers employ strands of 2-24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag+ can be achieved by optimizing solution conditions. These Ag+-mediated duplexes are stable to at least 60 mM Mg2+, higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag+-mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag+-mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated ‘frames’ with WC paired ‘pictures’.

  8. Membrane protein crystallization in micelles conjugated by nucleoside base-pairing: A different concept.

    PubMed

    Hosamani, Basavaprabhu; Kale, Raju R; Sharma, Hemlata; Wachtel, Ellen; Kesselman, Ellina; Danino, Dganit; Friedman, Noga; Sheves, Mordechai; Namboothiri, Irishi N N; Patchornik, Guy

    2016-09-01

    The dearth of high quality, three dimensional crystals of membrane proteins, suitable for X-ray diffraction analysis, constitutes a serious barrier to progress in structural biology. To address this challenge, we have developed a new crystallization medium that relies on the conjugation of surfactant micelles via base-pairing of complementary hydrophobic nucleosides. Base-pairs formed at the interface between micelles bring them into proximity with each other; and when the conjugated micelles contain a membrane protein, crystal nucleation centers can be stabilized, thereby promoting crystal growth. Accordingly, two hydrophobic nucleoside derivatives - deoxyguanosine (G) and deoxycytidine (C), each covalently bonded to a 10 carbon chain were synthesized and added to an aqueous solution containing octyl β-d-thioglucopyranoside micelles. These hydrophobic nucleosides induced the formation of oil-rich globules after 2days incubation at 19°C or after a few hours in the presence of ammonium sulfate; however, phase separation was inhibited by 100mM GMP. The presence of the membrane protein bacteriorhodopsin in the conjugated - micellar dispersion resulted in the growth within the colorless globules of a variety of purple crystals, the color indicating a functional protein. On this basis, we suggest that conjugation of micelles via base-pair complementarity may provide significant assistance to the structural determination of integral membrane proteins. PMID:27368128

  9. Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

    PubMed

    Zgarbová, Marie; Otyepka, Michal; Šponer, Jiří; Lankaš, Filip; Jurečka, Petr

    2014-08-12

    Terminal base pairs of DNA and RNA molecules in solution are known to undergo frequent transient opening events (fraying). Accurate modeling of this process is important because of its involvement in nucleic acid end recognition and enzymatic catalysis. In this article, we describe fraying in molecular dynamics simulations with the ff99bsc0, ff99bsc0χOL3, and ff99bsc0χOL4 force fields, both for DNA and RNA molecules. Comparison with the experiment showed that while some features of fraying are consistent with the available data, others indicate potential problems with the force field description. In particular, multiple noncanonical structures are formed at the ends of the DNA and RNA duplexes. Among them are tWC/sugar edge pair, C-H edge/Watson-Crick pair, and stacked geometries, in which the terminal bases are stacked above each other. These structures usually appear within the first tens to hundreds of nanoseconds and substantially limit the usefulness of the remaining part of the simulation due to geometry distortions that are transferred to several neighboring base pairs ("end effects"). We show that stability of the noncanonical structures in ff99bsc0 may be partly linked to inaccurate glycosidic (χ) torsion potentials that overstabilize the syn region and allow for rapid anti to syn transitions. The RNA refined glycosidic torsion potential χOL3 provides an improved description and substantially more stable MD simulations of RNA molecules. In the case of DNA, the χOL4 correction gives only partial improvement. None of the tested force fields provide a satisfactory description of the terminal regions, indicating that further improvement is needed to achieve realistic modeling of fraying in DNA and RNA molecules. PMID:26588288

  10. Reversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair

    NASA Astrophysics Data System (ADS)

    Kaul, Corinna; Müller, Markus; Wagner, Mirko; Schneider, Sabine; Carell, Thomas

    2011-10-01

    The universal genetic code relies on two hydrogen-bonded Watson-Crick base pairs that can form 64 triplet codons. This places a limit on the number of amino acids that can be encoded, which has motivated efforts to create synthetic base pairs that are orthogonal to the natural ones. An additional base pair would result in another 61 triplet codons. Artificial organic base pairs have been described in enzymatic incorporation studies, and inorganic T-Hg-T and C-Ag-C base pairs have been reported to form in primer extension studies. Here, we demonstrate a metal base pair that is fully orthogonal and can be replicated, and can even be amplified by polymerase chain reaction in the presence of the canonical pairs dA:dT and dG:dC. Crystal structures of a dS-Cu-dS base pair inside a polymerase show that reversible chemistry is possible directly inside the polymerase, which enables the efficient copying of the inorganic crosslink. The results open up the possibility of replicating and amplifying artificial inorganic DNA nanostructures by extending the genetic alphabet.

  11. High efficient key-insulated attribute based encryption scheme without bilinear pairing operations.

    PubMed

    Hong, Hanshu; Sun, Zhixin

    2016-01-01

    Attribute based encryption (ABE) has been widely applied for secure data protection in various data sharing systems. However, the efficiency of existing ABE schemes is not high enough since running encrypt and decrypt algorithms need frequent bilinear pairing operations, which may occupy too much computing resources on terminal devices. What's more, since different users may share the same attributes in the system, a single user's private key exposure will threaten the security and confidentiality of the whole system. Therefore, to further decrease the computation cost in attribute based cryptosystem as well as provide secure protection when key exposure happens, in this paper, we firstly propose a high efficient key-insulated ABE algorithm without pairings. The key-insulated mechanism guarantees both forward security and backward security when key exposure or user revocation happens. Besides, during the running of algorithms in our scheme, users and attribute authority needn't run any bilinear pairing operations, which will increase the efficiency to a large extent. The high efficiency and security analysis indicate that our scheme is more appropriate for secure protection in data sharing systems.

  12. Detecting pairing symmetry in Fe-based superconductors: Solitons and proximity patch

    NASA Astrophysics Data System (ADS)

    Vakaryuk, Victor; Stanev, Valentin; Lee, Wei-Cheng; Levchenko, Alex

    2013-03-01

    We suggest a mechanism which promotes the existence of a phase soliton - topological defect formed in the relative phase of superconducting gaps of a two-band superconductor with s+ - type of pairing. This mechanism exploits the proximity effect with a conventional s-wave superconductor which favors the alignment of the phases of the two-band superconductor which, in the case of s+ - pairing, are π-shifted in the absence of proximity. In the case of a strong proximity such effect can be used to reduce soliton's energy below the energy of a soliton-free state thus making the soliton thermodynamically stable. Based on this observation we consider an experimental setup, applicable both for stable and metastable solitons, which can be used to distinguish between s+ - and s+ + types of pairing in the iron-based multiband superconductors. The financial support was provided by the Center of Emergent Superconductivity funded by the U.S. DOE, Award No. DE-AC0298CH1088. W.C.L. acknowledges Roving Postdoc Program sponsored by CES. AL acknowledges support from Michigan State University.

  13. Effect of base-pair stability of nearest-neighbor nucleotides on the fidelity of deoxyribonucleic acid synthesis.

    PubMed

    Patten, J E; So, A G; Downey, K M

    1984-04-10

    The influence of the stability of base pairs formed by nearest-neighbor nucleotides on misincorporation frequency has been studied with the large fragment of DNA polymerase I, the alternating DNA copolymers, poly(dI-dC) and poly-(dG-dC), as template-primers, and dGTP, dITP, and dCTP as substrates. We have utilized the difference in thermodynamic stability between the doubly H-bonded I X C base pair and triply H-bonded G X C base pair to examine the effects of base-pair stability of both the "preceding" and the "following" nucleotides on the frequency of insertion of a mismatched nucleotide, as well as on its stable incorporation into polynucleotide. The present studies demonstrate that the stability of the base pairs formed by nearest-neighbor nucleotides affects the frequency of incorporation of noncomplementary nucleotides. Misincorporation frequency is increased when the nearest-neighbor nucleotides form more stable base pairs with the corresponding nucleotides in the template and is decreased when they form less stable base pairs. The stability of the base pair formed by a nucleotide either preceding (5' to) or following (3' to) a misincorporated nucleotide influences misincorporation frequency, but by different mechanisms. The stability of base pairs formed by preceding nucleotides affects the rate of insertion of mismatched nucleotide but does not protect the mismatched nucleotide from removal by the 3' to 5' exonuclease activity. In contrast, the stability of a base pair formed by a following nucleotide determines whether a misincorporated nucleotide is extended or excised by affecting the ability of the enzyme to edit errors of incorporation. PMID:6722115

  14. Orbital-Parity Selective Superconducting Pairing Structures of Fe-based Superconductors under Glide Symmetry

    NASA Astrophysics Data System (ADS)

    Lin, Chiahui; Chou, Chung-Pin; Yin, Wei-Guo; Ku, Wei

    2014-03-01

    We show that the superconductivity in Fe-based superconductors consists of zero and finite momentum (π , π , 0) Cooper pairs with the same and different parities of the Fe 3 d orbitals respectively. The former develops the distinct gap structures for each orbital parity, and the latter is characteristic of spin singlet, spacial oddness and time reversal symmetry breaking. This originates from the unit cell containing two Fe atoms and two anions of staggered positioning with respect to the Fe square lattice. The in-plane translation is turned into glide translation, which dictates orbital-parity selective quasiparticles. Such novel pairing structures explain the unusual gap angular modulation on the hole pockets in recent ARPES and STS experiments. Work supported by DOE DE-AC02-98CH10886 and Chinese Academy of Engineering Physics and Ministry of Science and Technology.

  15. Increasing Occurrences and Functional Roles for High Energy Purine-Pyrimidine Base-Pairs in Nucleic Acids

    PubMed Central

    Kimsey, Isaac; Al-Hashimi, Hashim M.

    2014-01-01

    There are a growing number of studies reporting the observation of purine-pyrimidine base-pairs that are seldom observed in unmodified nucleic acids because they entail the loss of energetically favorable interactions or require energetically costly base ionization or tautomerization. These high energy purine-pyrimidine base-pairs include G•C+ and A•T Hoogsteen base-pairs, which entail ~180° rotation of the purine base in a Watson-Crick base-pair, protonation of cytosine N3, and constriction of the C1′–C1′ distance by ~2.5 Å. Other high energy pure-pyrimidine base-pairs include G•T, G•U, and A•C mispairs that adopt Watson-Crick like geometry through either base ionization or tautomerization. Although difficult to detect and characterize using biophysical methods, high energy purine-pyrimidine base-pairs appear to be more common than once thought. They further expand the structural and functional diversity of canonical and noncanonical nucleic acid base-pairs. PMID:24721455

  16. Using gap symmetry and structure to reveal the pairing mechanism in Fe-based superconductors

    NASA Astrophysics Data System (ADS)

    Hirschfeld, Peter J.

    2016-01-01

    I review theoretical ideas and implications of experiments for the gap structure and symmetry of the Fe-based superconductors. Unlike any other class of unconventional superconductors, one has in these systems the possibility to tune the interactions by small changes in pressure, doping or disorder. Thus, measurements of order parameter evolution with these parameters should enable a deeper understanding of the underlying interactions. I briefly review the "standard paradigm" for s-wave pairing in these systems, and then focus on developments in the past several years which have challenged this picture. I further discuss the reasons for the apparent close competition between pairing in s- and d-wave channels, particularly in those systems where one type of Fermi surface pocket - hole or electron - is missing. Observation of a transition between s- and d-wave symmetry, possibly via a time reversal symmetry breaking "s + id" state, would provide an important confirmation of these ideas. Several proposals for detecting these novel phases are discussed, including the appearance of order parameter collective modes in Raman and optical conductivities. Transitions between two different types of s-wave states, involving various combinations of signs on Fermi surface pockets, can also proceed through a T-breaking "s + is" state. I discuss recent work that suggests pairing may take place away from the Fermi level over a surprisingly large energy range, as well as the effect of glide plane symmetry of the Fe-based systems on the superconductivity, including various exotic, time and translational invariance breaking pair states that have been proposed. Finally, I address disorder issues, and the various ways systematic introduction of disorder can (and cannot) be used to extract information on gap symmetry and structure.

  17. Adjacent segment disease.

    PubMed

    Virk, Sohrab S; Niedermeier, Steven; Yu, Elizabeth; Khan, Safdar N

    2014-08-01

    EDUCATIONAL OBJECTIVES As a result of reading this article, physicians should be able to: 1. Understand the forces that predispose adjacent cervical segments to degeneration. 2. Understand the challenges of radiographic evaluation in the diagnosis of cervical and lumbar adjacent segment disease. 3. Describe the changes in biomechanical forces applied to adjacent segments of lumbar vertebrae with fusion. 4. Know the risk factors for adjacent segment disease in spinal fusion. Adjacent segment disease (ASD) is a broad term encompassing many complications of spinal fusion, including listhesis, instability, herniated nucleus pulposus, stenosis, hypertrophic facet arthritis, scoliosis, and vertebral compression fracture. The area of the cervical spine where most fusions occur (C3-C7) is adjacent to a highly mobile upper cervical region, and this contributes to the biomechanical stress put on the adjacent cervical segments postfusion. Studies have shown that after fusion surgery, there is increased load on adjacent segments. Definitive treatment of ASD is a topic of continuing research, but in general, treatment choices are dictated by patient age and degree of debilitation. Investigators have also studied the risk factors associated with spinal fusion that may predispose certain patients to ASD postfusion, and these data are invaluable for properly counseling patients considering spinal fusion surgery. Biomechanical studies have confirmed the added stress on adjacent segments in the cervical and lumbar spine. The diagnosis of cervical ASD is complicated given the imprecise correlation of radiographic and clinical findings. Although radiological and clinical diagnoses do not always correlate, radiographs and clinical examination dictate how a patient with prolonged pain is treated. Options for both cervical and lumbar spine ASD include fusion and/or decompression. Current studies are encouraging regarding the adoption of arthroplasty in spinal surgery, but more long

  18. Base pairing and structural insights into the 5-formylcytosine in RNA duplex.

    PubMed

    Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O; Chen, Doris; Sheng, Jia

    2016-06-01

    5-Formylcytidine (f(5)C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m(5)C) through 5-hydroxymethylcytidine (hm(5)C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f(5)C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5'-GUA(f(5)C)GUAC-3']2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f(5)C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

  19. Base pairing and structural insights into the 5-formylcytosine in RNA duplex

    PubMed Central

    Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O.; Chen, Doris; Sheng, Jia

    2016-01-01

    5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

  20. Characterizing a Wake-Free Safe Zone for the Simplified Aircraft-Based Paired Approach Concept

    NASA Technical Reports Server (NTRS)

    Guerreiro, Nelson M.; Neitzke, Kurt W.; Johnson, Sally C.; Stough, H. Paul, III; McKissick, Burnell T.; Syed, Hazari I.

    2010-01-01

    The Federal Aviation Administration (FAA) has proposed a concept of operations geared towards achieving increased arrival throughput at U.S. Airports, known as the Simplified Aircraft-based Paired Approach (SAPA) concept. In this study, a preliminary characterization of a wake-free safe zone (WFSZ) for the SAPA concept has been performed. The experiment employed Monte-Carlo simulations of varying approach profiles by aircraft pairs to closely-spaced parallel runways. Three different runway lateral spacings were investigated (750 ft, 1000 ft and 1400 ft), along with no stagger and 1500 ft stagger between runway thresholds. The paired aircraft were flown in a leader/trailer configuration with potential wake encounters detected using a wake detection surface translating with the trailing aircraft. The WFSZ is characterized in terms of the smallest observed initial in-trail distance leading to a wake encounter anywhere along the approach path of the aircraft. The results suggest that the WFSZ can be characterized in terms of two primary altitude regions, in ground-effect (IGE) and out of ground-effect (OGE), with the IGE region being the limiting case with a significantly smaller WFSZ. Runway stagger was observed to only modestly reduce the WFSZ size, predominantly in the OGE region.

  1. Origin of Asymmetry of Paired Nanogap Voltammograms Based on Scanning Electrochemical Microscopy: Contamination Not Adsorption.

    PubMed

    Chen, Ran; Balla, Ryan J; Li, Zhiting; Liu, Haitao; Amemiya, Shigeru

    2016-08-16

    Formation of a nanometer-wide gap between tip and substrate electrodes by scanning electrochemical microscopy (SECM) enables voltammetric measurement of ultrafast electron-transfer kinetics. Herein, we demonstrate the advantage of SECM-based nanogap voltammetry to assess the cleanness of the substrate surface in solution by confirming that airborne contamination of highly oriented pyrolytic graphite (HOPG) causes the nonideal asymmetry of paired nanogap voltammograms of (ferrocenylmethyl)trimethylammonium (Fc(+)). We hypothesize that the amperometric response of a 1 μm-diameter Pt tip is less enhanced in the feedback mode, where more hydrophilic Fc(2+) is generated from Fc(+) at the tip and reduced voltammetrically at the HOPG surface covered with airborne hydrophobic contaminants. The tip current is more enhanced in the substrate generation/tip collection mode, where less charged Fc(+) is oxidized at the contaminated HOPG surface. In fact, symmetric pairs of nanogap voltammograms are obtained with the cleaner HOPG surface that is exfoliated in humidified air and covered with a nanometer-thick water adlayer to suppress airborne contamination. This result disproves a misconception that the asymmetry of paired nanogap voltammograms is due to electron exchange mediated by Fc(2+) adsorbed on the glass sheath of the tip. Moreover, weak Fc(+) adsorption on the HOPG surface causes only the small hysteresis of each voltammogram upon forward and reverse sweeps of the HOPG potential. Significantly, no Fc(2+) adsorption on the HOPG surface ensures that the simple outer-sphere pathway mediates ultrafast electron transfer of the Fc(2+/+) couple with standard rate constants of ≥12 cm/s as estimated from symmetric pairs of reversible nanogap voltammograms.

  2. A dual-wavelength erbium-doped fiber laser based on fiber grating pair

    NASA Astrophysics Data System (ADS)

    Sun, Hongwei; Wang, Tianshu; Jia, Qingsong; Zhang, Peng; Jiang, Huilin

    2014-12-01

    A dual-wavelength linear cavity erbium-doped fiber (EDF) laser based on a fiber grating pair is demonstrated experimentally. A circulator, a 980nm/1550nm wavelength division multiplexing (WDM) coupler, a 1×2 coupler, a polarization controller, a 6m long erbium-doped fiber and a fiber grating pair for wavelength interval of 0.3nm are included in the structure. A circulator connected at two ports as reflecting mirror structure. A 980nm pump source pump an erbium-doped fiber with a length of 6m consist of an erbium doped fiber amplifier. Through adjusting the state of the polarization controller, the transmission characteristic of cavity is changed. In both polarization and wavelength, the feedback from the fiber grating pair results in the laser operating on two longitudinal modes that are separated. The birefringence induced by the fiber grating pair is beneficial to diversify the polarization states of different wavelength in the erbium-doped fiber. So it is enhanced the polarization hole burning effect. This polarization hole burning effect greatly reduced the wavelength competition. Then, it was possible to achieve stable dual-wavelength. It turns out the structure generated the stable dual-wavelength with the 0.3nm wavelength interval and the output power is 0.13dBm in the end. The whole system have a simple and compact structure, it can work stably and laid a foundation for microwave/millimeter wave generator. It has a good application performance in the future for scientific research and daily life.

  3. Natural-Like Replication of an Unnatural Base Pair for the Expansion of the Genetic Alphabet and Biotechnology Applications

    PubMed Central

    Li, Lingjun; Degardin, Mélissa; Lavergne, Thomas; Malyshev, Denis A.; Dhami, Kirandeep; Ordoukhanian, Phillip

    2014-01-01

    We synthesized a panel of unnatural base pairs whose pairing depends on hydrophobic and packing forces and identify dTPT3-dNaM, which is PCR amplified with a natural base pair-like efficiency and fidelity. In addition, the dTPT3 scaffold is uniquely tolerant of attaching a propargyl amine linker, resulting in the dTPT3PA-dNaM pair, which is amplified only slightly less well. The identification of dTPT3 represents significant progress towards developing an unnatural base pair for the in vivo expansion of an organism's genetic alphabet and for a variety of in vitro biotechnology applications where it is used to site-specifically label amplified DNA, and it also demonstrates for the first time that hydrophobic and packing forces are sufficient to mediate natural-like replication. PMID:24152106

  4. Efficient and provable secure pairing-free security-mediated identity-based identification schemes.

    PubMed

    Chin, Ji-Jian; Tan, Syh-Yuan; Heng, Swee-Huay; Phan, Raphael C-W

    2014-01-01

    Security-mediated cryptography was first introduced by Boneh et al. in 2001. The main motivation behind security-mediated cryptography was the capability to allow instant revocation of a user's secret key by necessitating the cooperation of a security mediator in any given transaction. Subsequently in 2003, Boneh et al. showed how to convert a RSA-based security-mediated encryption scheme from a traditional public key setting to an identity-based one, where certificates would no longer be required. Following these two pioneering papers, other cryptographic primitives that utilize a security-mediated approach began to surface. However, the security-mediated identity-based identification scheme (SM-IBI) was not introduced until Chin et al. in 2013 with a scheme built on bilinear pairings. In this paper, we improve on the efficiency results for SM-IBI schemes by proposing two schemes that are pairing-free and are based on well-studied complexity assumptions: the RSA and discrete logarithm assumptions.

  5. Efficient and Provable Secure Pairing-Free Security-Mediated Identity-Based Identification Schemes

    PubMed Central

    Chin, Ji-Jian; Tan, Syh-Yuan; Heng, Swee-Huay; Phan, Raphael C.-W.

    2014-01-01

    Security-mediated cryptography was first introduced by Boneh et al. in 2001. The main motivation behind security-mediated cryptography was the capability to allow instant revocation of a user's secret key by necessitating the cooperation of a security mediator in any given transaction. Subsequently in 2003, Boneh et al. showed how to convert a RSA-based security-mediated encryption scheme from a traditional public key setting to an identity-based one, where certificates would no longer be required. Following these two pioneering papers, other cryptographic primitives that utilize a security-mediated approach began to surface. However, the security-mediated identity-based identification scheme (SM-IBI) was not introduced until Chin et al. in 2013 with a scheme built on bilinear pairings. In this paper, we improve on the efficiency results for SM-IBI schemes by proposing two schemes that are pairing-free and are based on well-studied complexity assumptions: the RSA and discrete logarithm assumptions. PMID:25207333

  6. Efficient and provable secure pairing-free security-mediated identity-based identification schemes.

    PubMed

    Chin, Ji-Jian; Tan, Syh-Yuan; Heng, Swee-Huay; Phan, Raphael C-W

    2014-01-01

    Security-mediated cryptography was first introduced by Boneh et al. in 2001. The main motivation behind security-mediated cryptography was the capability to allow instant revocation of a user's secret key by necessitating the cooperation of a security mediator in any given transaction. Subsequently in 2003, Boneh et al. showed how to convert a RSA-based security-mediated encryption scheme from a traditional public key setting to an identity-based one, where certificates would no longer be required. Following these two pioneering papers, other cryptographic primitives that utilize a security-mediated approach began to surface. However, the security-mediated identity-based identification scheme (SM-IBI) was not introduced until Chin et al. in 2013 with a scheme built on bilinear pairings. In this paper, we improve on the efficiency results for SM-IBI schemes by proposing two schemes that are pairing-free and are based on well-studied complexity assumptions: the RSA and discrete logarithm assumptions. PMID:25207333

  7. Enol tautomers of Watson-Crick base pair models are metastable because of nuclear quantum effects.

    PubMed

    Pérez, Alejandro; Tuckerman, Mark E; Hjalmarson, Harold P; von Lilienfeld, O Anatole

    2010-08-25

    Intermolecular enol tautomers of Watson-Crick base pairs could emerge spontaneously via interbase double proton transfer. It has been hypothesized that their formation could be facilitated by thermal fluctuations and proton tunneling, and possibly be relevant to DNA damage. Theoretical and computational studies, assuming classical nuclei, have confirmed the dynamic stability of these rare tautomers. However, by accounting for nuclear quantum effects explicitly through Car-Parrinello path integral molecular dynamics calculations, we find the tautomeric enol form to be dynamically metastable, with lifetimes too insignificant to be implicated in DNA damage. PMID:20681591

  8. Mass spectrometry based on a coupled Cooper-pair box and nanomechanical resonator system

    PubMed Central

    2011-01-01

    Nanomechanical resonators (NRs) with very high frequency have a great potential for mass sensing with unprecedented sensitivity. In this study, we propose a scheme for mass sensing based on the NR capacitively coupled to a Cooper-pair box (CPB) driven by two microwave currents. The accreted mass landing on the resonator can be measured conveniently by tracking the resonance frequency shifts because of mass changes in the signal absorption spectrum. We demonstrate that frequency shifts induced by adsorption of ten 1587 bp DNA molecules can be well resolved in the absorption spectrum. Integration with the CPB enables capacitive readout of the mechanical resonance directly on the chip. PMID:22039926

  9. Superior coexistence: systematicALLY regulatING land subsidence BASED on set pair theory

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Gong, S.-L.

    2015-11-01

    Anthropogenic land subsidence is an environmental side effect of exploring and using natural resources in the process of economic development. The key points of the system for controlling land subsidence include cooperation and superior coexistence while the economy develops, exploring and using natural resources, and geological environmental safety. Using the theory and method of set pair analysis (SPA), this article anatomises the factors, effects, and transformation of land subsidence. Based on the principle of superior coexistence, this paper promotes a technical approach to the system for controlling land subsidence, in order to improve the prevention and control of geological hazards.

  10. A Multiparty Controlled Bidirectional Quantum Secure Direct Communication and Authentication Protocol Based on EPR Pairs

    NASA Astrophysics Data System (ADS)

    Chang, Yan; Zhang, Shi-Bin; Yan, Li-Li; Sheng, Zhi-Wei

    2013-06-01

    A multiparty controlled bidirectional quantum secure direct communication and authentication protocol is proposed based on EPR pair and entanglement swapping. The legitimate identities of communicating parties are encoded to Bell states which act as a detection sequence. Secret messages are transmitted by using the classical XOR operation, which serves as a one-time-pad. No photon with secret information transmits in the quantum channel. Compared with the protocols proposed by Wang et al. [Acta Phys. Sin. 56 (2007) 673; Opt. Commun. 266 (2006) 732], the protocol in this study implements bidirectional communication and authentication, which defends most attacks including the ‘man-in-the-middle’ attack efficiently.

  11. Chemistry of stannylene-based Lewis pairs: dynamic tin coordination switching between donor and acceptor character.

    PubMed

    Krebs, Kilian M; Freitag, Sarah; Schubert, Hartmut; Gerke, Birgit; Pöttgen, Rainer; Wesemann, Lars

    2015-03-16

    The coordination chemistry of cyclic stannylene-based intramolecular Lewis pairs is presented. The P→Sn adducts were treated with [Ni(COD)2] and [Pd(PCy3)2] (COD = 1,5-cyclooctadiene, PCy3 = tricyclohexylphosphine). In the isolated coordination compounds the stannylene moiety acts either as an acceptor or a donor ligand. Examples of a dynamic switch between these two coordination modes of the P-Sn ligand are illustrated and the structures in the solid state together with heteronuclear NMR spectroscopic findings are discussed. In the case of a Ni(0) complex, (119)Sn Mössbauer spectroscopy of the uncoordinated and coordinated phosphastannirane ligand is presented.

  12. Mass spectrometry based on a coupled Cooper-pair box and nanomechanical resonator system

    NASA Astrophysics Data System (ADS)

    Jiang, Cheng; Chen, Bin; Li, Jin-Jin; Zhu, Ka-Di

    2011-10-01

    Nanomechanical resonators (NRs) with very high frequency have a great potential for mass sensing with unprecedented sensitivity. In this study, we propose a scheme for mass sensing based on the NR capacitively coupled to a Cooper-pair box (CPB) driven by two microwave currents. The accreted mass landing on the resonator can be measured conveniently by tracking the resonance frequency shifts because of mass changes in the signal absorption spectrum. We demonstrate that frequency shifts induced by adsorption of ten 1587 bp DNA molecules can be well resolved in the absorption spectrum. Integration with the CPB enables capacitive readout of the mechanical resonance directly on the chip.

  13. Powered Tate Pairing Computation

    NASA Astrophysics Data System (ADS)

    Kang, Bo Gyeong; Park, Je Hong

    In this letter, we provide a simple proof of bilinearity for the eta pairing. Based on it, we show an efficient method to compute the powered Tate pairing as well. Although efficiency of our method is equivalent to that of the Tate pairing on the eta pairing approach, but ours is more general in principle.

  14. Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA

    PubMed Central

    Hagan, Michael F.; Dinner, Aaron R.; Chandler, David; Chakraborty, Arup K.

    2003-01-01

    We combine free-energy calculations and molecular dynamics to elucidate a mechanism for DNA base-pair binding and unbinding in atomic detail. Specifically, transition-path sampling is used to overcome computational limitations associated with conventional techniques to harvest many trajectories for the flipping of a terminal cytosine in a 3-bp oligomer in explicit water. Comparison with free-energy projections obtained with umbrella sampling reveals four coordinates that separate true dynamic transition states from stable reactant and product states. Unbinding proceeds via two qualitatively different pathways: one in which the flipping base breaks its intramolecular hydrogen bonds before it unstacks and another in which it ruptures both sets of interactions simultaneously. Both on- and off-pathway intermediates are observed. The relation of the results to coarse-grained models for DNA-based biosensors is discussed. PMID:14617777

  15. Role of Pre-rRNA Base Pairing and 80S Complex Formation in Subnucleolar Localization of the U3 snoRNP

    PubMed Central

    Granneman, Sander; Vogelzangs, Judith; Lührmann, Reinhard; van Venrooij, Walther J.; Pruijn, Ger J. M.; Watkins, Nicholas J.

    2004-01-01

    In the nucleolus the U3 snoRNA is recruited to the 80S pre-rRNA processing complex in the dense fibrillar component (DFC). The U3 snoRNA is found throughout the nucleolus and has been proposed to move with the preribosomes to the granular component (GC). In contrast, the localization of other RNAs, such as the U8 snoRNA, is restricted to the DFC. Here we show that the incorporation of the U3 snoRNA into the 80S processing complex is not dependent on pre-rRNA base pairing sequences but requires the B/C motif, a U3-specific protein-binding element. We also show that the binding of Mpp10 to the 80S U3 complex is dependent on sequences within the U3 snoRNA that base pair with the pre-rRNA adjacent to the initial cleavage site. Furthermore, mutations that inhibit 80S complex formation and/or the association of Mpp10 result in retention of the U3 snoRNA in the DFC. From this we propose that the GC localization of the U3 snoRNA is a direct result of its active involvement in the initial steps of ribosome biogenesis. PMID:15367679

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

    PubMed

    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.

  17. Yeast Pif1 Helicase Exhibits a One-base-pair Stepping Mechanism for Unwinding Duplex DNA*

    PubMed Central

    Ramanagoudr-Bhojappa, Ramanagouda; Chib, Shubeena; Byrd, Alicia K.; Aarattuthodiyil, Suja; Pandey, Manjula; Patel, Smita S.; Raney, Kevin D.

    2013-01-01

    Kinetic analysis of the DNA unwinding and translocation activities of helicases is necessary for characterization of the biochemical mechanism(s) for this class of enzymes. Saccharomyces cerevisiae Pif1 helicase was characterized using presteady state kinetics to determine rates of DNA unwinding, displacement of streptavidin from biotinylated DNA, translocation on single-stranded DNA (ssDNA), and ATP hydrolysis activities. Unwinding of substrates containing varying duplex lengths was fit globally to a model for stepwise unwinding and resulted in an unwinding rate of ∼75 bp/s and a kinetic step size of 1 base pair. Pif1 is capable of displacing streptavidin from biotinylated oligonucleotides with a linear increase in the rates as the length of the oligonucleotides increased. The rate of translocation on ssDNA was determined by measuring dissociation from varying lengths of ssDNA and is essentially the same as the rate of unwinding of dsDNA, making Pif1 an active helicase. The ATPase activity of Pif1 on ssDNA was determined using fluorescently labeled phosphate-binding protein to measure the rate of phosphate release. The quantity of phosphate released corresponds to a chemical efficiency of 0.84 ATP/nucleotides translocated. Hence, when all of the kinetic data are considered, Pif1 appears to move along DNA in single nucleotide or base pair steps, powered by hydrolysis of 1 molecule of ATP. PMID:23596008

  18. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

    NASA Technical Reports Server (NTRS)

    Urakawa, Hidetoshi; El Fantroussi, Said; Smidt, Hauke; Smoot, James C.; Tribou, Erik H.; Kelly, John J.; Noble, Peter A.; Stahl, David A.

    2003-01-01

    The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

  19. Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing

    PubMed Central

    Li, Sanshu; Breaker, Ronald R.

    2013-01-01

    Thiamin pyrophosphate (TPP) riboswitches are found in organisms from all three domains of life. Examples in bacteria commonly repress gene expression by terminating transcription or by blocking ribosome binding, whereas most eukaryotic TPP riboswitches are predicted to regulate gene expression by modulating RNA splicing. Given the widespread distribution of eukaryotic TPP riboswitches and the diversity of their locations in precursor messenger RNAs (pre-mRNAs), we sought to examine the mechanism of alternative splicing regulation by a fungal TPP riboswitch from Neurospora crassa, which is mostly located in a large intron separating protein-coding exons. Our data reveal that this riboswitch uses a long-distance (∼530-nt separation) base-pairing interaction to regulate alternative splicing. Specifically, a portion of the TPP-binding aptamer can form a base-paired structure with a conserved sequence element (α) located near a 5′ splice site, which greatly increases use of this 5′ splice site and promotes gene expression. Comparative sequence analyses indicate that many fungal species carry a TPP riboswitch with similar intron architecture, and therefore the homologous genes in these fungi are likely to use the same mechanism. Our findings expand the scope of genetic control mechanisms relying on long-range RNA interactions to include riboswitches. PMID:23376932

  20. Simulation Based on Negative ion pair Techniques of Electric propulsion In Satellite Mission Using Chlorine Gas

    NASA Astrophysics Data System (ADS)

    Bakkiyaraj, R.

    R.Bakkiyaraj,Assistant professor,Government college of Engineering ,Bargur,Tamilnadu. *C.Sathiyavel, PG Student and Department of Aeronautical Engineering/Branch of Avionics, PSN college of Engineering and Technology,Tirunelveli,India. Abstract: Ion propulsion rocket system is expected to become popular with the development of ion-ion pair techniques because of their stimulated of low propellant, Design of repulsive between negative ions with low electric power and high efficiency. A Negative ion pair of ion propulsion rocket system is proposed in this work .Negative Ion Based Rocket system consists of three parts 1.ionization chamber 2. Repulsion force and ion accelerator 3. Exhaust of Nozzle. The Negative ions from electro negatively gas are produced by attachment of the gas ,such as chlorine with electron emitted from a Electron gun ionization chamber. The formulate of large stable negative ion is achievable in chlorine gas with respect to electron affinity (∆E). When a neutral chlorine atom in the gaseous form picks up an electron to form a cl- ion, it releases energy of 349 kJ/mol or 3.6 eV/atom. It is said to have an electron affinity of -349 kJ/mol ,the negative sign indicating that energy is released during this process .The distance between negative ions pair is important for the evaluation of the rocket thrust and is also determined by the exhaust velocity of the propellant. The mass flow rate of ions is related to the ion beam current. Accelerate the Negative ions to a high velocity in the thrust vector direction with a significantly intense grids and the exhaust of negative ions through Nozzle. The simulation of the ion propulsion system has been carried out by MATLAB. By comparing the simulation results with the theoretical and previous results, we have found that the proposed method is achieved of thrust value with low electric power for simulating the ion propulsion rocket system

  1. Evaluating changes in matrix based, recovery-adjusted concentrations in paired data for pesticides in groundwater

    USGS Publications Warehouse

    Zimmerman, Tammy M.; Breen, Kevin J.

    2012-01-01

    Pesticide concentration data for waters from selected carbonate-rock aquifers in agricultural areas of Pennsylvania were collected in 1993–2009 for occurrence and distribution assessments. A set of 30 wells was visited once in 1993–1995 and again in 2008–2009 to assess concentration changes. The data include censored matched pairs (nondetections of a compound in one or both samples of a pair). A potentially improved approach for assessing concentration changes is presented where (i) concentrations are adjusted with models of matrix-spike recovery and (ii) area-wide temporal change is tested by use of the paired Prentice-Wilcoxon (PPW) statistical test. The PPW results for atrazine, simazine, metolachlor, prometon, and an atrazine degradate, deethylatrazine (DEA), are compared using recovery-adjusted and unadjusted concentrations. Results for adjusted compared with unadjusted concentrations in 2008–2009 compared with 1993–1995 were similar for atrazine and simazine (significant decrease; 95% confidence level) and metolachlor (no change) but differed for DEA (adjusted, decrease; unadjusted, increase) and prometon (adjusted, decrease; unadjusted, no change). The PPW results were different on recovery-adjusted compared with unadjusted concentrations. Not accounting for variability in recovery can mask a true change, misidentify a change when no true change exists, or assign a direction opposite of the true change in concentration that resulted from matrix influences on extraction and laboratory method performance. However, matrix-based models of recovery derived from a laboratory performance dataset from multiple studies for national assessment, as used herein, rather than time- and study-specific recoveries may introduce uncertainty in recovery adjustments for individual samples that should be considered in assessing change.

  2. Theory of nodal s±-wave pairing symmetry in the Pu-based 115 superconductor family

    PubMed Central

    Das, Tanmoy; Zhu, Jian-Xin; Graf, Matthias J.

    2015-01-01

    The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-Tc superconductors and predict the presence of a nodal s+− wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scattering channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s+− wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry. PMID:25721375

  3. Theory of nodal s±-wave pairing symmetry in the Pu-based 115 superconductor family

    SciTech Connect

    Das, Tanmoy; Zhu, Jian -Xin; Graf, Matthias J.

    2015-02-27

    The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-Tc superconductors and predict the presence of a nodal s⁺⁻ wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scattering channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s⁺⁻ wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry.

  4. Theory of nodal s±-wave pairing symmetry in the Pu-based 115 superconductor family

    DOE PAGES

    Das, Tanmoy; Zhu, Jian -Xin; Graf, Matthias J.

    2015-02-27

    The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-Tc superconductors and predict the presence of a nodal s⁺⁻ wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scattering channel,more » which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s⁺⁻ wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry.« less

  5. Role of the Closing Base Pair for d(GCA) Hairpin Stability: Free Energy Analysis and Folding Simulations

    SciTech Connect

    Kannan, Srinivasaraghavan; Zacharias, Martin W.

    2011-06-30

    Hairpin loops belong to the most important structural motifs in folded nucleic acids. The d(GNA) sequence in DNA can form very stable trinucleotide hairpin loops depending, however, strongly on the closing base pair. Replica-exchange molecular dynamics (REMD) were employed to study hairpin folding of two DNA sequences, d(gcGCAgc) and d(cgGCAcg), with the same central loop motif but different closing base pairs starting from singlestranded structures. In both cases, conformations of the most populated conformational cluster at the lowest temperature showed close agreement with available experimental structures. For the loop sequence with the less stable G:C closing base pair, an alternative loop topology accumulated as second most populated conformational state indicating a possible loop structural heterogeneity. Comparative-free energy simulations on induced loop unfolding indicated higher stability of the loop with a C:G closing base pair by 3 kcal mol1 (compared to a G:C closing base pair) in very good agreement with experiment. The comparative energetic analysis of sampled unfolded, intermediate and folded conformational states identified electrostatic and packing interactions as the main contributions to the closing base pair dependence of the d(GCA) loop stability.

  6. A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA

    PubMed Central

    Kladwang, Wipapat; Cordero, Pablo; Das, Rhiju

    2011-01-01

    We present a rapid experimental strategy for inferring base pairs in structured RNAs via an information-rich extension of classic chemical mapping approaches. The mutate-and-map method, previously applied to a DNA/RNA helix, systematically searches for single mutations that enhance the chemical accessibility of base-pairing partners distant in sequence. To test this strategy for structured RNAs, we have carried out mutate-and-map measurements for a 35-nt hairpin, called the MedLoop RNA, embedded within an 80-nt sequence. We demonstrate the synthesis of all 105 single mutants of the MedLoop RNA sequence and present high-throughput DMS, CMCT, and SHAPE modification measurements for this library at single-nucleotide resolution. The resulting two-dimensional data reveal visually clear, punctate features corresponding to RNA base pair interactions as well as more complex features; these signals can be qualitatively rationalized by comparison to secondary structure predictions. Finally, we present an automated, sequence-blind analysis that permits the confident identification of nine of the 10 MedLoop RNA base pairs at single-nucleotide resolution, while discriminating against all 1460 false-positive base pairs. These results establish the accuracy and information content of the mutate-and-map strategy and support its feasibility for rapidly characterizing the base-pairing patterns of larger and more complex RNA systems. PMID:21239468

  7. Cloud Base Height Measurements at Manila Observatory: Initial Results from Constructed Paired Sky Imaging Cameras

    NASA Astrophysics Data System (ADS)

    Lagrosas, N.; Tan, F.; Antioquia, C. T.

    2014-12-01

    Fabricated all sky imagers are efficient and cost effective instruments for cloud detection and classification. Continuous operation of this instrument can result in the determination of cloud occurrence and cloud base heights for the paired system. In this study, a fabricated paired sky imaging system - consisting two commercial digital cameras (Canon Powershot A2300) enclosed in weatherproof containers - is developed in Manila Observatory for the purpose of determining cloud base heights at the Manila Observatory area. One of the cameras is placed on the rooftop of Manila Observatory and the other is placed on the rooftop of the university dormitory, 489m from the first camera. The cameras are programmed to simultaneously gather pictures every 5 min. Continuous operation of these cameras were implemented since the end of May of 2014 but data collection started end of October 2013. The data were processed following the algorithm proposed by Kassianov et al (2005). The processing involves the calculation of the merit function that determines the area of overlap of the two pictures. When two pictures are overlapped, the minimum of the merit function corresponds to the pixel column positions where the pictures have the best overlap. In this study, pictures of overcast sky prove to be difficult to process for cloud base height and were excluded from processing. The figure below shows the initial results of the hourly average of cloud base heights from data collected from November 2013 to July 2014. Measured cloud base heights ranged from 250m to 1.5km. These are the heights of cumulus and nimbus clouds that are dominant in this part of the world. Cloud base heights are low in the early hours of the day indicating low convection process during these times. However, the increase in the convection process in the atmosphere can be deduced from higher cloud base heights in the afternoon. The decrease of cloud base heights after 15:00 follows the trend of decreasing solar

  8. The selective tRNA aminoacylation mechanism based on a single G•U pair.

    PubMed

    Naganuma, Masahiro; Sekine, Shun-ichi; Chong, Yeeting Esther; Guo, Min; Yang, Xiang-Lei; Gamper, Howard; Hou, Ya-Ming; Schimmel, Paul; Yokoyama, Shigeyuki

    2014-06-26

    Ligation of tRNAs with their cognate amino acids, by aminoacyl-tRNA synthetases, establishes the genetic code. Throughout evolution, tRNA(Ala) selection by alanyl-tRNA synthetase (AlaRS) has depended predominantly on a single wobble base pair in the acceptor stem, G3•U70, mainly on the kcat level. Here we report the crystal structures of an archaeal AlaRS in complex with tRNA(Ala) with G3•U70 and its A3•U70 variant. AlaRS interacts with both the minor- and the major-groove sides of G3•U70, widening the major groove. The geometry difference between G3•U70 and A3•U70 is transmitted along the acceptor stem to the 3'-CCA region. Thus, the 3'-CCA region of tRNA(Ala) with G3•U70 is oriented to the reactive route that reaches the active site, whereas that of the A3•U70 variant is folded back into the non-reactive route. This novel mechanism enables the single wobble pair to dominantly determine the specificity of tRNA selection, by an approximate 100-fold difference in kcat.

  9. GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

    PubMed

    Nemoto, Wataru; Yamanishi, Yoshihiro; Limviphuvadh, Vachiranee; Saito, Akira; Toh, Hiroyuki

    2016-09-01

    G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-dimers or higher-order molecular complexes. Many GPCRs exert a wide variety of molecular functions by forming specific combinations of GPCR subtypes. In addition, some GPCRs are reportedly associated with diseases. GPCR oligomerization is now recognized as an important event in various biological phenomena, and many researchers are investigating this subject. We have developed a support vector machine (SVM)-based method to predict interacting pairs for GPCR oligomerization, by integrating the structure and sequence information of GPCRs. The performance of our method was evaluated by the Receiver Operating Characteristic (ROC) curve. The corresponding area under the curve was 0.938. As far as we know, this is the only prediction method for interacting pairs among GPCRs. Our method could accelerate the analyses of these interactions, and contribute to the elucidation of the global structures of the GPCR networks in membranes. Proteins 2016; 84:1224-1233. © 2016 Wiley Periodicals, Inc. PMID:27191053

  10. Peptide tag/probe pairs based on the coordination chemistry for protein labeling.

    PubMed

    Uchinomiya, Shohei; Ojida, Akio; Hamachi, Itaru

    2014-02-17

    Protein-labeling methods serve as essential tools for analyzing functions of proteins of interest under complicated biological conditions such as in live cells. These labeling methods are useful not only to fluorescently visualize proteins of interest in biological systems but also to conduct protein and cell analyses by harnessing the unique functions of molecular probes. Among the various labeling methods available, an appropriate binding pair consisting of a short peptide and a de novo designed small molecular probe has attracted attention because of its wide utility and versatility. Interestingly, most peptide tag/probe pairs exploit metal-ligand coordination interactions as the main binding force responsible for their association. Herein, we provide an overview of the recent progress of these coordination-chemistry-based protein-labeling methods and their applications for fluorescence imaging and functional analysis of cellular proteins, while highlighting our originally developed labeling methods. These successful examples clearly exemplify the utility and versatility of metal coordination chemistry in protein functional analysis.

  11. Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition

    PubMed Central

    Kuznetsov, Nikita A.; Bergonzo, Christina; Campbell, Arthur J.; Li, Haoquan; Mechetin, Grigory V.; de los Santos, Carlos; Grollman, Arthur P.; Fedorova, Olga S.; Zharkov, Dmitry O.; Simmerling, Carlos

    2015-01-01

    Formamidopyrimidine-DNA glycosylase (Fpg) excises 8-oxoguanine (oxoG) from DNA but ignores normal guanine. We combined molecular dynamics simulation and stopped-flow kinetics with fluorescence detection to track the events in the recognition of oxoG by Fpg and its mutants with a key phenylalanine residue, which intercalates next to the damaged base, changed to either alanine (F110A) or fluorescent reporter tryptophan (F110W). Guanine was sampled by Fpg, as evident from the F110W stopped-flow traces, but less extensively than oxoG. The wedgeless F110A enzyme could bend DNA but failed to proceed further in oxoG recognition. Modeling of the base eversion with energy decomposition suggested that the wedge destabilizes the intrahelical base primarily through buckling both surrounding base pairs. Replacement of oxoG with abasic (AP) site rescued the activity, and calculations suggested that wedge insertion is not required for AP site destabilization and eversion. Our results suggest that Fpg, and possibly other DNA glycosylases, convert part of the binding energy into active destabilization of their substrates, using the energy differences between normal and damaged bases for fast substrate discrimination. PMID:25520195

  12. Fingerprint identification using SIFT-based minutia descriptors and improved all descriptor-pair matching.

    PubMed

    Zhou, Ru; Zhong, Dexing; Han, Jiuqiang

    2013-01-01

    The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT) descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1) the similar patterns of parallel ridges; and (2) high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD) to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM), is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA) achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements. PMID:23467056

  13. Fingerprint Identification Using SIFT-Based Minutia Descriptors and Improved All Descriptor-Pair Matching

    PubMed Central

    Zhou, Ru; Zhong, Dexing; Han, Jiuqiang

    2013-01-01

    The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT) descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1) the similar patterns of parallel ridges; and (2) high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD) to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM), is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA) achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements. PMID:23467056

  14. Fingerprint identification using SIFT-based minutia descriptors and improved all descriptor-pair matching.

    PubMed

    Zhou, Ru; Zhong, Dexing; Han, Jiuqiang

    2013-03-06

    The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT) descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1) the similar patterns of parallel ridges; and (2) high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD) to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM), is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA) achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements.

  15. Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings.

    PubMed

    Keepers, J W; Kollman, P A; Weiner, P K; James, T L

    1982-09-01

    Molecular mechanics studies have been carried out on "B-DNA-like" structures of [d(C-G-C-G-A-A-T-T-C-G-C-G)](2) and [d(A)](12).[d(T)](12). Each of the backbone torsion angles (psi, phi, omega, omega', phi') has been "forced" to alternative values from the normal B-DNA values (g(+), t, g(-), g(-), t conformations). Compensating torsion angle changes preserve most of the base stacking energy in the double helix. In a second part of the study, one purine N3-pyrimidine N1 distance at a time has been forced to a value of 6 A in an attempt to simulate the base opening motions required to rationalize proton exchange data for DNA. When the 6-A constraint is removed, many of the structures revert to the normal Watson-Crick hydrogen-bonded structure, but a number are trapped in structures approximately 5 kcal/mol higher in energy than the starting B-DNA structure. The relative energy of these structures, some of which involve a non-Watson-Crick thymine C2(carbonyl)[unk]adenine 6NH(2) hydrogen bond, are qualitatively consistent with the DeltaH for a "base pair-open state" suggested by Mandal et al. of 4-6 kcal/mol [Mandal, C., Kallenbach, N. R. & Englander, S. W. (1979) J. Mol. Biol. 135, 391-411]. The picture of DNA flexibility emerging from this study depicts the backbone as undergoing rapid motion between local torsional minima on a nanosecond time scale. Backbone motion is mainly localized within a dinucleoside segment and generally not conformationally coupled along the chain or across the base pairs. Base motions are much smaller in magnitude than backbone motions. Base sliding allows imino N-H exchange, but it is localized, and only a small fraction of the N-H groups is exposed at any one time. Stacking and hydrogen bonding cause a rigid core of bases in the center of the molecule accounting for the hydrodynamic properties of DNA.

  16. A likelihood-based reconstruction algorithm for top-quark pairs and the KLFitter framework

    NASA Astrophysics Data System (ADS)

    Erdmann, Johannes; Guindon, Stefan; Kröninger, Kevin; Lemmer, Boris; Nackenhorst, Olaf; Quadt, Arnulf; Stolte, Philipp

    2014-06-01

    A likelihood-based reconstruction algorithm for arbitrary event topologies is introduced and, as an example, applied to the single-lepton decay mode of top-quark pair production. The algorithm comes with several options which further improve its performance, in particular the reconstruction efficiency, i.e., the fraction of events for which the observed jets and leptons can be correctly associated with the final-state particles of the corresponding event topology. The performance is compared to that of well-established reconstruction algorithms using a common framework for kinematic fitting. This framework has a modular structure which describes the physics processes and detector models independently. The implemented algorithms are generic and can easily be ported from one experiment to another.

  17. Single-base pair differences in a shared motif determine differential Rhodopsin expression.

    PubMed

    Rister, Jens; Razzaq, Ansa; Boodram, Pamela; Desai, Nisha; Tsanis, Cleopatra; Chen, Hongtao; Jukam, David; Desplan, Claude

    2015-12-01

    The final identity and functional properties of a neuron are specified by terminal differentiation genes, which are controlled by specific motifs in compact regulatory regions. To determine how these sequences integrate inputs from transcription factors that specify cell types, we compared the regulatory mechanism of Drosophila Rhodopsin genes that are expressed in subsets of photoreceptors to that of phototransduction genes that are expressed broadly, in all photoreceptors. Both sets of genes share an 11-base pair (bp) activator motif. Broadly expressed genes contain a palindromic version that mediates expression in all photoreceptors. In contrast, each Rhodopsin exhibits characteristic single-bp substitutions that break the symmetry of the palindrome and generate activator or repressor motifs critical for restricting expression to photoreceptor subsets. Sensory neuron subtypes can therefore evolve through single-bp changes in short regulatory motifs, allowing the discrimination of a wide spectrum of stimuli.

  18. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

    PubMed Central

    2016-01-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  19. The influence of arene-ring size on stacking interaction with canonical base pairs

    NASA Astrophysics Data System (ADS)

    Formánek, Martin; Burda, Jaroslav V.

    2014-04-01

    Stacking interactions between aromatic molecules (benzene, p-cymene, biphenyl, and di- and tetra-hydrogen anthracene) and G.C and A.T canonical Watson-Crick (WC) base pairs are explored. Two functionals with dispersion corrections: ω-B97XD and B3LYP-D3 are used. For a comparison also the MP2 and B3LYP-D3/PCM methods were used for the most stable p-cymene…WC geometries. It was found that the stacking interaction increases with the size of π-conjugation system. Its extent is in agreement with experimental finding on anticancer activity of Ru(II) piano-stool complexes where intercalation of these aromatic molecules should play an important role. The explored structures are considered as ternary system so that decomposition of the interaction energy to pairwise and non-additivity contributions is also examined.

  20. Single base pair differences in a shared motif determine differential Rhodopsin expression

    PubMed Central

    Rister, Jens; Razzaq, Ansa; Boodram, Pamela; Desai, Nisha; Tsanis, Cleopatra; Chen, Hongtao; Jukam, David; Desplan, Claude

    2016-01-01

    The final identity and functional properties of a neuron are specified by terminal differentiation genes, which are controlled by specific motifs in compact regulatory regions. To determine how these sequences integrate inputs from transcription factors that specify cell types, we compared the regulatory mechanism of Drosophila Rhodopsin genes that are expressed in subsets of photoreceptors to that of phototransduction genes that are expressed broadly, in all photoreceptors. Both sets of genes share an 11bp activator motif. Broadly expressed genes contain a palindromic version that mediates expression in all photoreceptors. In contrast, each Rhodopsin exhibits unique single bp substitutions that break the symmetry of the palindrome and generate activator or repressor motifs critical for restricting expression to photoreceptor subsets. Novel sensory neuron subtypes can therefore evolve through single base pair changes in short regulatory motifs, allowing the discrimination of a wide spectrum of stimuli. PMID:26785491

  1. Prediction of multidimensional drug dose responses based on measurements of drug pairs

    PubMed Central

    Zimmer, Anat; Katzir, Itay; Dekel, Erez; Alon, Uri

    2016-01-01

    Finding potent multidrug combinations against cancer and infections is a pressing therapeutic challenge; however, screening all combinations is difficult because the number of experiments grows exponentially with the number of drugs and doses. To address this, we present a mathematical model that predicts the effects of three or more antibiotics or anticancer drugs at all doses based only on measurements of drug pairs at a few doses, without need for mechanistic information. The model provides accurate predictions on available data for antibiotic combinations, and on experiments presented here on the response matrix of three cancer drugs at eight doses per drug. This approach offers a way to search for effective multidrug combinations using a small number of experiments. PMID:27562164

  2. Intriguing radical-radical interactions among double-electron oxidized adenine-thymine base pairs

    NASA Astrophysics Data System (ADS)

    Wang, Mei; Zhao, Jing; Zhang, Laibin; Su, Xiyu; Su, Hanlei; Bu, Yuxiang

    2015-01-01

    We present a theoretical investigation of the structural and electronic properties of double-electron oxidized adenine-thymine base pair as well as its deprotonated Watson-Crick derivatives. Double-electron oxidation can destabilize the AT unit, leading to a barrier-hindered metastable A+T+ state with a dissociation channel featuring negative dissociation energy. This unusual energetic phenomenon originates from the competition of electrostatic repulsion and attractively hydrogen-bonding interaction co-existing between Arad + and Trad +. The associated double-proton-transfer process is also explored, suggesting a possible two-step mechanism. Magnetic coupling interactions of various diradical structures are controlled by both intra- and inter-molecular interactions.

  3. Wavelet transform based on the optimal wavelet pairs for tunable diode laser absorption spectroscopy signal processing.

    PubMed

    Li, Jingsong; Yu, Benli; Fischer, Horst

    2015-04-01

    This paper presents a novel methodology-based discrete wavelet transform (DWT) and the choice of the optimal wavelet pairs to adaptively process tunable diode laser absorption spectroscopy (TDLAS) spectra for quantitative analysis, such as molecular spectroscopy and trace gas detection. The proposed methodology aims to construct an optimal calibration model for a TDLAS spectrum, regardless of its background structural characteristics, thus facilitating the application of TDLAS as a powerful tool for analytical chemistry. The performance of the proposed method is verified using analysis of both synthetic and observed signals, characterized with different noise levels and baseline drift. In terms of fitting precision and signal-to-noise ratio, both have been improved significantly using the proposed method.

  4. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses

    NASA Technical Reports Server (NTRS)

    Urakawa, Hidetoshi; Noble, Peter A.; El Fantroussi, Said; Kelly, John J.; Stahl, David A.

    2002-01-01

    The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T(d)) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5' terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T(d) and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T(d) and signal intensity, and it decreased the variability of the signal. Although T(d)s of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T(d)s than those with mismatches in the first or second position. The trained NNs predicted the T(d) with high accuracies (R(2) = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R(2) = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T(d)s, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5' terminus plays a greater role in determining the T(d) and signal intensity of duplexes than the type of mismatch.

  5. Kinetic selection vs. free energy of DNA base pairing in control of polymerase fidelity.

    PubMed

    Oertell, Keriann; Harcourt, Emily M; Mohsen, Michael G; Petruska, John; Kool, Eric T; Goodman, Myron F

    2016-04-19

    What is the free energy source enabling high-fidelity DNA polymerases (pols) to favor incorporation of correct over incorrect base pairs by 10(3)- to 10(4)-fold, corresponding to free energy differences of ΔΔGinc∼ 5.5-7 kcal/mol? Standard ΔΔG° values (∼0.3 kcal/mol) calculated from melting temperature measurements comparing matched vs. mismatched base pairs at duplex DNA termini are far too low to explain pol accuracy. Earlier analyses suggested that pol active-site steric constraints can amplify DNA free energy differences at the transition state (kinetic selection). A recent paper [Olson et al. (2013)J Am Chem Soc135:1205-1208] used Vent pol to catalyze incorporations in the presence of inorganic pyrophosphate intended to equilibrate forward (polymerization) and backward (pyrophosphorolysis) reactions. A steady-state leveling off of incorporation profiles at long reaction times was interpreted as reaching equilibrium between polymerization and pyrophosphorolysis, yielding apparent ΔG° = -RTlnKeq, indicating ΔΔG° of 3.5-7 kcal/mol, sufficient to account for pol accuracy without need of kinetic selection. Here we perform experiments to measure and account for pyrophosphorolysis explicitly. We show that forward and reverse reactions attain steady states far from equilibrium for wrong incorporations such as G opposite T. Therefore,[Formula: see text]values obtained from such steady-state evaluations ofKeqare not dependent on DNA properties alone, but depend largely on constraints imposed on right and wrong substrates in the polymerase active site.

  6. Kinetic selection vs. free energy of DNA base pairing in control of polymerase fidelity

    PubMed Central

    Oertell, Keriann; Harcourt, Emily M.; Mohsen, Michael G.; Petruska, John; Kool, Eric T.; Goodman, Myron F.

    2016-01-01

    What is the free energy source enabling high-fidelity DNA polymerases (pols) to favor incorporation of correct over incorrect base pairs by 103- to 104-fold, corresponding to free energy differences of ΔΔGinc ∼ 5.5–7 kcal/mol? Standard ΔΔG° values (∼0.3 kcal/mol) calculated from melting temperature measurements comparing matched vs. mismatched base pairs at duplex DNA termini are far too low to explain pol accuracy. Earlier analyses suggested that pol active-site steric constraints can amplify DNA free energy differences at the transition state (kinetic selection). A recent paper [Olson et al. (2013) J Am Chem Soc 135:1205–1208] used Vent pol to catalyze incorporations in the presence of inorganic pyrophosphate intended to equilibrate forward (polymerization) and backward (pyrophosphorolysis) reactions. A steady-state leveling off of incorporation profiles at long reaction times was interpreted as reaching equilibrium between polymerization and pyrophosphorolysis, yielding apparent ΔG° = −RT ln Keq, indicating ΔΔG° of 3.5–7 kcal/mol, sufficient to account for pol accuracy without need of kinetic selection. Here we perform experiments to measure and account for pyrophosphorolysis explicitly. We show that forward and reverse reactions attain steady states far from equilibrium for wrong incorporations such as G opposite T. Therefore, ΔΔGinc° values obtained from such steady-state evaluations of Keq are not dependent on DNA properties alone, but depend largely on constraints imposed on right and wrong substrates in the polymerase active site. PMID:27044101

  7. Hydrogen-bonded proton transfer in the protonated guanine-cytosine (GC+H)+ base pair.

    PubMed

    Lin, Yuexia; Wang, Hongyan; Gao, Simin; Schaefer, Henry F

    2011-10-13

    The single proton transfer at the different sites of the Watson-Crick (WC) guanine-cytosine (GC) DNA base pair are studied here using density functional methods. The conventional protonated structures, transition state (TS) and proton-transferred product (PT) structures of every relevant species are optimized. Each transition state and proton-transferred product structure has been compared with the corresponding conventional protonated structure to demonstrate the process of proton transfer and the change of geometrical structures. The relative energies of the protonated tautomers and the proton-transfer energy profiles in gas and solvent are analyzed. The proton-transferred product structure G(+H(+))-H(+)C(N3)(-H(+))(PT) has the lowest relative energy for which only two hydrogen bonds exist. Almost all 14 isomers of the protonated GC base pair involve hydrogen-bonded proton transfer following the three pathways, with the exception of structure G-H(+)C(O2). When the positive charge is primarily "located" on the guanine moiety (H(+)G-C, G-H(+)C(C4), and G-H(+)C(C6)), the H(1) proton transfers from the N(1) site of guanine to the N(3) site of cytosine. The structures G-H(+)C(C5) and G-H(+)C(C4) involve H(4a) proton transfer from the N(4) of cytosine to the O(6) site of guanine. H(2a) proton transfer from the N(2) site of guanine to the O(2) site of cytosine is found only for the structure G-H(+)C(C4). The structures to which a proton is added on the six-centered sites adjoining the hydrogen bonds are more prone to proton transfer in the gas phase, whereas a proton added on the minor groove and the sites adjoining the hydrogen bonds is favorable to the proton transfer in energy in the aqueous phase.

  8. Kinetic selection vs. free energy of DNA base pairing in control of polymerase fidelity.

    PubMed

    Oertell, Keriann; Harcourt, Emily M; Mohsen, Michael G; Petruska, John; Kool, Eric T; Goodman, Myron F

    2016-04-19

    What is the free energy source enabling high-fidelity DNA polymerases (pols) to favor incorporation of correct over incorrect base pairs by 10(3)- to 10(4)-fold, corresponding to free energy differences of ΔΔGinc∼ 5.5-7 kcal/mol? Standard ΔΔG° values (∼0.3 kcal/mol) calculated from melting temperature measurements comparing matched vs. mismatched base pairs at duplex DNA termini are far too low to explain pol accuracy. Earlier analyses suggested that pol active-site steric constraints can amplify DNA free energy differences at the transition state (kinetic selection). A recent paper [Olson et al. (2013)J Am Chem Soc135:1205-1208] used Vent pol to catalyze incorporations in the presence of inorganic pyrophosphate intended to equilibrate forward (polymerization) and backward (pyrophosphorolysis) reactions. A steady-state leveling off of incorporation profiles at long reaction times was interpreted as reaching equilibrium between polymerization and pyrophosphorolysis, yielding apparent ΔG° = -RTlnKeq, indicating ΔΔG° of 3.5-7 kcal/mol, sufficient to account for pol accuracy without need of kinetic selection. Here we perform experiments to measure and account for pyrophosphorolysis explicitly. We show that forward and reverse reactions attain steady states far from equilibrium for wrong incorporations such as G opposite T. Therefore,[Formula: see text]values obtained from such steady-state evaluations ofKeqare not dependent on DNA properties alone, but depend largely on constraints imposed on right and wrong substrates in the polymerase active site. PMID:27044101

  9. Characterization of the Trans Watson-Crick GU Base Pair Located in the Catalytic Core of the Antigenomic HDV Ribozyme

    PubMed Central

    Lévesque, Dominique; Reymond, Cédric; Perreault, Jean-Pierre

    2012-01-01

    The HDV ribozyme’s folding pathway is, by far, the most complex folding pathway elucidated to date for a small ribozyme. It includes 6 different steps that have been shown to occur before the chemical cleavage. It is likely that other steps remain to be discovered. One of the most critical of these unknown steps is the formation of the trans Watson-Crick GU base pair within loop III. The U23 and G28 nucleotides that form this base pair are perfectly conserved in all natural variants of the HDV ribozyme, and therefore are considered as being part of the signature of HDV-like ribozymes. Both the formation and the transformation of this base pair have been studied mainly by crystal structure and by molecular dynamic simulations. In order to obtain physical support for the formation of this base pair in solution, a set of experiments, including direct mutagenesis, the site-specific substitution of chemical groups, kinetic studies, chemical probing and magnesium-induced cleavage, were performed with the specific goal of characterizing this trans Watson-Crick GU base pair in an antigenomic HDV ribozyme. Both U23 and G28 can be substituted for nucleotides that likely preserve some of the H-bond interactions present before and after the cleavage step. The formation of the more stable trans Watson-Crick base pair is shown to be a post-cleavage event, while a possibly weaker trans Watson-Crick/Hoogsteen interaction seems to form before the cleavage step. The formation of this unusually stable post-cleavage base pair may act as a driving force on the chemical cleavage by favouring the formation of a more stable ground state of the product-ribozyme complex. To our knowledge, this represents the first demonstration of a potential stabilising role of a post-cleavage conformational switch event in a ribozyme-catalyzed reaction. PMID:22768274

  10. Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions

    PubMed Central

    2006-01-01

    Tertiary interactions are crucial in maintaining the tRNA structure and functionality. We used a combined sequence analysis and quantum mechanics approach to calculate accurate energies of the most frequent tRNA tertiary base pairing interactions. Our analysis indicates that six out of the nine classical tertiary interactions are held in place mainly by H-bonds between the bases. In the remaining three cases other effects have to be considered. Tertiary base pairing interaction energies range from −8 to −38 kcal/mol in yeast tRNAPhe and are estimated to contribute roughly 25% of the overall tRNA base pairing interaction energy. Six analyzed posttranslational chemical modifications were shown to have minor effect on the geometry of the tertiary interactions. Modifications that introduce a positive charge strongly stabilize the corresponding tertiary interactions. Non-additive effects contribute to the stability of base triplets. PMID:16461956

  11. Current hormonal contraceptive use predicts female extra-pair and dyadic sexual behavior: evidence based on Czech National Survey data.

    PubMed

    Klapilová, Kateřina; Cobey, Kelly D; Wells, Timothy; Roberts, S Craig; Weiss, Petr; Havlíček, Jan

    2014-01-10

    Data from 1155 Czech women (493 using oral contraception, 662 non-users), obtained from the Czech National Survey of Sexual Behavior, were used to investigate evolutionary-based hypotheses concerning the predictive value of current oral contraceptive (OC) use on extra-pair and dyadic (in-pair) sexual behavior of coupled women. Specifically, the aim was to determine whether current OC use was associated with lower extra-pair and higher in-pair sexual interest and behavior, because OC use suppresses cyclical shifts in mating psychology that occur in normally cycling women. Zero-inflated Poisson (ZIP) regression and negative binomial models were used to test associations between OC use and these sexual measures, controlling for other relevant predictors (e.g., age, parity, in-pair sexual satisfaction, relationship length). The overall incidence of having had an extra-pair partner or one-night stand in the previous year was not related to current OC use (the majority of the sample had not). However, among the women who had engaged in extra-pair sexual behavior, OC users had fewer one-night stands than non-users, and tended to have fewer partners, than non-users. OC users also had more frequent dyadic intercourse than non-users, potentially indicating higher commitment to their current relationship. These results suggest that suppression of fertility through OC use may alter important aspects of female sexual behavior, with potential implications for relationship functioning and stability.

  12. Prediction of contact residue pairs based on co-substitution between sites in protein structures.

    PubMed

    Miyazawa, Sanzo

    2013-01-01

    Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints in varying degrees on each residue site. Selective constraints on residue sites are recorded in amino acid orders in homologous sequences and also in the evolutionary trace of amino acid substitutions. A challenge is to extract direct dependences between residue sites by removing phylogenetic correlations and indirect dependences through other residues within a protein or even through other molecules. Rapid growth of protein families with unknown folds requires an accurate de novo prediction method for protein structure. Recent attempts of disentangling direct from indirect dependences of amino acid types between residue positions in multiple sequence alignments have revealed that inferred residue-residue proximities can be sufficient information to predict a protein fold without the use of known three-dimensional structures. Here, we propose an alternative method of inferring coevolving site pairs from concurrent and compensatory substitutions between sites in each branch of a phylogenetic tree. Substitution probability and physico-chemical changes (volume, charge, hydrogen-bonding capability, and others) accompanied by substitutions at each site in each branch of a phylogenetic tree are estimated with the likelihood of each substitution, and their direct correlations between sites are used to detect concurrent and compensatory substitutions. In order to extract direct dependences between sites, partial correlation coefficients of the characteristic changes along branches between sites, in which linear multiple dependences on feature vectors at other sites are removed, are calculated and used to rank coevolving site pairs. Accuracy of contact prediction based on the present coevolution score is comparable to that achieved by a maximum entropy model of protein sequences for 15 protein families

  13. biobambam: tools for read pair collation based algorithms on BAM files

    PubMed Central

    2014-01-01

    Background Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. Results In this paper we introduce biobambam, a set of tools based on the efficient collation of alignments in BAM files by read name. The employed collation algorithm avoids time and space consuming sorting of alignments by read name where this is possible without using more than a specified amount of main memory. Using this algorithm tasks like duplicate marking in BAM files and conversion of BAM files to the FastQ format can be performed very efficiently with limited resources. We also make the collation algorithm available in the form of an API for other projects. This API is part of the libmaus package. Conclusions In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities our approach can often perform an equivalent task more efficiently in terms of the required main memory and run-time. Our BAM to FastQ conversion is faster than all widely known alternatives including Picard and bamUtil. Our duplicate marking is about as fast as the closest competitor bamUtil for small data sets and faster than all known alternatives on large and complex data sets.

  14. The computation of cloud base height from paired whole-sky imaging cameras

    SciTech Connect

    Allmen, M.C.; Kegelmeyer, W.P. Jr.

    1994-03-01

    A major goal for global change studies is to improve the accuracy of general circulation models (GCMs) capable of predicting the timing and magnitude of greenhouse gas-induced global warming. Research has shown that cloud radiative feedback is the single most important effect determining the magnitude of possible climate responses to human activity. Of particular value to reducing the uncertainties associated with cloud-radiation interactions is the measurement of cloud base height (CBH), both because it is a dominant factor in determining the infrared radiative properties of clouds with respect to the earth`s surface and lower atmosphere and because CBHs are essential to measuring cloud cover fraction. We have developed a novel approach to the extraction of cloud base height from pairs of whole sky imaging (WSI) cameras. The core problem is to spatially register cloud fields from widely separated WSI cameras; this complete, triangulation provides the CBH measurements. The wide camera separation (necessary to cover the desired observation area) and the self-similarity of clouds defeats all standard matching algorithms when applied to static views of the sky. To address this, our approach is based on optical flow methods that exploit the fact that modern WSIs provide sequences of images. We will describe the algorithm and present its performance as evaluated both on real data validated by ceilometer measurements and on a variety of simulated cases.

  15. Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

    PubMed Central

    Kacmarczyk, Thadeous J.; Ishii, Jennifer; Betel, Doron; Alonso, Alicia; Mason, Christopher E.; Figueroa, Maria E.; Melnick, Ari M.

    2015-01-01

    DNA methylation pattern mapping is heavily studied in normal and diseased tissues. A variety of methods have been established to interrogate the cytosine methylation patterns in cells. Reduced representation of whole genome bisulfite sequencing was developed to detect quantitative base pair resolution cytosine methylation patterns at GC-rich genomic loci. This is accomplished by combining the use of a restriction enzyme followed by bisulfite conversion. Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) increases the biologically relevant genomic loci covered and has been used to profile cytosine methylation in DNA from human, mouse and other organisms. ERRBS initiates with restriction enzyme digestion of DNA to generate low molecular weight fragments for use in library preparation. These fragments are subjected to standard library construction for next generation sequencing. Bisulfite conversion of unmethylated cytosines prior to the final amplification step allows for quantitative base resolution of cytosine methylation levels in covered genomic loci. The protocol can be completed within four days. Despite low complexity in the first three bases sequenced, ERRBS libraries yield high quality data when using a designated sequencing control lane. Mapping and bioinformatics analysis is then performed and yields data that can be easily integrated with a variety of genome-wide platforms. ERRBS can utilize small input material quantities making it feasible to process human clinical samples and applicable in a range of research applications. The video produced demonstrates critical steps of the ERRBS protocol. PMID:25742437

  16. Novel H⁺-Ion Sensor Based on a Gated Lateral BJT Pair.

    PubMed

    Yuan, Heng; Zhang, Jixing; Cao, Chuangui; Zhang, Gangyuan; Zhang, Shaoda

    2015-01-01

    An H⁺-ion sensor based on a gated lateral bipolar junction transistor (BJT) pair that can operate without the classical reference electrode is proposed. The device is a special type of ion-sensitive field-effect transistor (ISFET). Classical ISFETs have the advantage of miniaturization, but  they are difficult to fabricate by a single fabrication process because of the bulky and brittle reference electrode materials. Moreover, the reference electrodes need to be separated from the sensor device in some cases. The proposed device is composed of two gated lateral BJT components, one of which had a silicide layer while the other was without the layer. The two components were operated under the metal-oxide semiconductor field-effect transistor (MOSFET)-BJT hybrid mode, which can be controlled by emitter voltage and base current. Buffer solutions with different pH values were used as the sensing targets to verify the characteristics of the proposed device. Owing to their different sensitivities, both components could simultaneously detect the H⁺-ion concentration and function as a reference to each other. Per the experimental results, the sensitivity of the proposed device was found to be approximately 0.175 μA/pH. This experiment demonstrates enormous potential to lower the cost of the ISFET-based sensor technology. PMID:26703625

  17. Analysis of Vision Loss Caused by Radiation-Induced Optic Neuropathy After Particle Therapy for Head-and-Neck and Skull-Base Tumors Adjacent to Optic Nerves

    SciTech Connect

    Demizu, Yusuke; Murakami, Masao; Miyawaki, Daisuke; Niwa, Yasue; Akagi, Takashi; Sasaki, Ryohei; Terashima, Kazuki; Suga, Daisaku; Kamae, Isao; Hishikawa, Yoshio

    2009-12-01

    Purpose: To assess the incident rates of vision loss (VL; based on counting fingers or more severe) caused by radiation-induced optic neuropathy (RION) after particle therapy for tumors adjacent to optic nerves (ONs), and to evaluate factors that may contribute to VL. Methods and Materials: From August 2001 to August 2006, 104 patients with head-and-neck or skull-base tumors adjacent to ONs were treated with carbon ion or proton radiotherapy. Among them, 145 ONs of 75 patients were irradiated and followed for greater than 12 months. The incident rate of VL and the prognostic factors for occurrence of VL were evaluated. The late effects of carbon ion and proton beams were compared on the basis of a biologically effective dose at alpha/beta = 3 gray equivalent (GyE{sub 3}). Results: Eight patients (11%) experienced VL resulting from RION. The onset of VL ranged from 17 to 58 months. The median follow-up was 25 months. No significant difference was observed between the carbon ion and proton beam treatment groups. On univariate analysis, age (>60 years), diabetes mellitus, and maximum dose to the ON (>110 GyE{sub 3}) were significant, whereas on multivariate analysis only diabetes mellitus was found to be significant for VL. Conclusions: The time to the onset of VL was highly variable. There was no statistically significant difference between carbon ion and proton beam treatments over the follow-up period. Based on multivariate analysis, diabetes mellitus correlated with the occurrence of VL. A larger study with longer follow-up is warranted.

  18. Seismic structure beneath the Gulf of Aqaba and adjacent areas based on the tomographic inversion of regional earthquake data

    NASA Astrophysics Data System (ADS)

    El Khrepy, Sami; Koulakov, Ivan; Al-Arifi, Nassir; Petrunin, Alexey G.

    2016-06-01

    We present the first 3-D model of seismic P and S velocities in the crust and uppermost mantle beneath the Gulf of Aqaba and surrounding areas based on the results of passive travel time tomography. The tomographic inversion was performed based on travel time data from ˜ 9000 regional earthquakes provided by the Egyptian National Seismological Network (ENSN), and this was complemented with data from the International Seismological Centre (ISC). The resulting P and S velocity patterns were generally consistent with each other at all depths. Beneath the northern part of the Red Sea, we observed a strong high-velocity anomaly with abrupt limits that coincide with the coastal lines. This finding may indicate the oceanic nature of the crust in the Red Sea, and it does not support the concept of gradual stretching of the continental crust. According to our results, in the middle and lower crust, the seismic anomalies beneath the Gulf of Aqaba seem to delineate a sinistral shift (˜ 100 km) in the opposite flanks of the fault zone, which is consistent with other estimates of the left-lateral displacement in the southern part of the Dead Sea Transform fault. However, no displacement structures were visible in the uppermost lithospheric mantle.

  19. Occurrence and severity of enamel decalcification adjacent to bracket bases and sub-bracket lesions during orthodontic treatment with two different lingual appliances

    PubMed Central

    Klang, Elisabeth; Helms, Hans-Joachim; Wiechmann, Dirk

    2016-01-01

    Summary Background: Using lingual enamel surfaces for bracket placement not only has esthetic advantages, but may also be suitable in terms of reducing frequencies of enamel decalcifications. Objective: To test the null-hypothesis that there is no significant difference in enamel decalcification or cavitation incidence adjacent to and beneath bracket bases between two lingual multi-bracket (MB) appliances that are different in terms of design, material composition, and manufacturing technology (group A: WIN, DW-LingualSystems; group B: Incognito, 3M-Unitek), taking into account patient- and treatment-related variables on white spot lesion (WSL) formation. Methods: Standardized, digital, top-view photographs of 630 consecutive subjects (16214 teeth; n Incognito = 237/6076 teeth; n WIN = 393/10138 teeth; mean age: 17.47±7.8; m/f 43.2/56.8%) with completed lingual MB treatment of the upper and lower permanent teeth 1–7 were screened for decalcification or cavitation adjacent to and beneath the bracket bases before and after treatment, scored from 0 to 7. Non-parametric ANOVA was used for main effects ‘appliance type’, ‘gender’, ‘treatment complexity’, ‘grouped age’ (≤16/>16 years), and ‘treatment duration’ as covariable, at an α-level of 5%. Results: About 2.57% [5.94%] of all teeth in group A [B] developed decalcifications. Subject-related incidence was 9.59% [16.17%] for upper incisors in group A [B], and 12.98% [25.74%] for all teeth 16–46. There were significant effects by gender, age, and treatment duration. Conclusion: The null-hypothesis was rejected: sub-bracket lesions were significantly less frequent in group A, while frequencies of WSL adjacent to brackets were not significantly affected by appliance type. In view of the overall low incidences of lingual post-orthodontic white-spot lesions, the use of lingual appliances is advocated as a valid strategy for a reduction of enamel decalcifications during orthodontic treatment. PMID

  20. Density functional theory studies of interactions of ruthenium-arene complexes with base pair steps.

    PubMed

    Mutter, Shaun T; Platts, James A

    2011-10-20

    Density functional theory (DFT) calculations have been performed to determine the strength and geometry of intermolecular interactions of "piano-stool" ruthenium arene complexes, which show potential as anticancer treatments. Model complexes with methane and benzene indicate that the coordinated arene has C-H···π acceptor ability similar to that of free benzene, whereas this arene acts as a much stronger C-H donor or partner in π-stacking than free benzene. The source of these enhanced interactions is identified as a combination of electrostatic and dispersion effects. Complexes of Ru-arene complexes with base-pair step fragments of DNA, in which the arene has the potential to act as an intercalator, have also been investigated. Binding energies are found to be sensitive to the size and nature of the arene, with larger and more flexible arenes having stronger binding. π-stacking and C-H···π interactions between arene and DNA bases and hydrogen bonds from coordinated N-H to DNA oxygen atoms, as well as covalent Ru-N bonding, contribute to the overall binding. The effect of complexation on DNA structure is also examined, with larger rise and more negative slide values than canonical B-DNA observed in all cases.

  1. Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

    PubMed

    Nikolova, Evgenia N; Goh, Garrett B; Brooks, Charles L; Al-Hashimi, Hashim M

    2013-05-01

    G·C Hoogsteen base pairs can form transiently in duplex DNA and play important roles in DNA recognition, replication, and repair. G·C Hoogsteen base pairs are thought to be stabilized by protonation of cytosine N3, which affords a second key hydrogen bond, but experimental evidence for this is sparse because the proton cannot be directly visualized by X-ray crystallography and nuclear magnetic resonance spectroscopy. Here, we combine NMR and constant pH molecular dynamics simulations to directly investigate the pKa of cytosine N3 in a chemically trapped N1-methyl-G·C Hoogsteen base pair within duplex DNA. Analysis of NMR chemical shift perturbations and NOESY data as a function of pH revealed that cytosine deprotonation is coupled to a syn-to-anti transition in N1-methyl-G, which results in a distorted Watson-Crick geometry at pH >9. A four-state analysis of the pH titration profiles yields a lower bound pKa estimate of 7.2 ± 0.1 for the G·C Hoogsteen base pair, which is in good agreement with the pKa value (7.1 ± 0.1) calculated independently using constant pH MD simulations. Based on these results and pH-dependent NMR relaxation dispersion measurements, we estimate that under physiological pH (pH 7-8), G·C Hoogsteen base pairs in naked DNA have a population of 0.02-0.002%, as compared to 0.4% for A·T Hoogsteen base pairs, and likely exist primarily as protonated species.

  2. High Levels of Transcription Stimulate Transversions at GC Base Pairs in Yeast

    PubMed Central

    Alexander, Matthew P.; Begins, Kaitlyn J.; Crall, William C.; Holmes, Margaret P.; Lippert, Malcolm J.

    2016-01-01

    High-levels of transcription through a gene stimulate spontaneous mutation rate, a phenomenon termed transcription-associated mutation (TAM). While transcriptional effects on specific mutation classes have been identified using forward mutation and frameshift-reversion assays, little is yet known about transcription-associated base substitutions in yeast. To address this issue, we developed a new base substitution reversion assay (the lys2-TAG allele). We report a 22-fold increase in overall reversion rate in the high- relative to the low-transcription strain (from 2.1- to 47- × 10−9). While all detectable base substitution types increased in the high-transcription strain, G→T and G→C transversions increased disproportionately by 58- and 52-fold, respectively. To assess a potential role of DNA damage in the TAM events, we measured mutation rates and spectra in individual strains defective in the repair of specific DNA lesions or null for the error-prone translesion DNA polymerase zeta (Pol zeta). Results exclude a role of 8-oxoGuanine, general oxidative damage, or apurinic/apyrimidinic sites in the generation of TAM G→T and G→C transversions. In contrast, the TAM transversions at GC base pairs depend on Pol zeta for occurrence implicating DNA damage, other than oxidative lesions or AP sites, in the TAM mechanism. Results further indicate that transcription-dependent G→T transversions in yeast differ mechanistically from equivalent events in E. coli reported by others. Given their occurrences in repair-proficient cells, transcription-associated G→T and G→C events represent a novel type of transcription-associated mutagenesis in normal cells with potentially important implications for evolution and genetic disease. PMID:23055242

  3. Formation and dissociation of protonated cytosine—cytosine base pairs in i-motifs by ab initio quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-Hu; Li, Ming; Wang, Yan-Ting; Ouyang, Zhong-Can

    2014-02-01

    Formation and dissociation mechanisms of C—C+ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C—C+ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C—C+ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.

  4. Nucleon-pair states of even-even Sn isotopes based on realistic effective interactions

    NASA Astrophysics Data System (ADS)

    Cheng, Y. Y.; Qi, C.; Zhao, Y. M.; Arima, A.

    2016-08-01

    In this paper we study yrast states of 128,126,124Sn and 104,106,108Sn by using the monopole-optimized realistic interactions in terms of both the shell model (SM) and the nucleon-pair approximation (NPA). For yrast states of 128,126Sn and 104,106Sn, we calculate the overlaps between the wave functions obtained in the full SM space and those obtained in the truncated NPA space, and find that most of these overlaps are very close to 1. Very interestingly, for most of these states with positive parity and even spin or with negative parity and odd spin, the SM wave function is found to be well represented by one nucleon-pair basis state, viz., a simple picture of "nucleon-pair states" (nucleon-pair configuration without mixings) emerges. In 128,126Sn, the positive-parity (or negative-parity) yrast states with spin J >10 (or J >7 ) are found to be well described by breaking one or two S pairs in the 101+ (or 71-) state, i.e., the yrast state of seniority-two, spin-maximum, and positive-parity (or negative-parity), into non-S pair(s). Similar regularity is also pointed out for 104,106Sn. The evolution of E 2 transition rates between low-lying states in 128,126,124Sn is discussed in terms of the seniority scheme.

  5. Prevalence of adjacent segment disc degeneration in patients undergoing anterior cervical discectomy and fusion based on pre-operative MRI findings.

    PubMed

    Lundine, Kristopher M; Davis, Gavin; Rogers, Myron; Staples, Margaret; Quan, Gerald

    2014-01-01

    Anterior cervical discectomy and fusion (ACDF) is a widely accepted surgical treatment for symptomatic cervical spondylosis. Some patients develop symptomatic adjacent segment degeneration, occasionally requiring further treatment. The cause and prevalence of adjacent segment degeneration and disease is unclear at present. Proponents for motion preserving surgery such as disc arthroplasty argue that this technique may decrease the "strain" on adjacent discs and thus decrease the incidence of symptomatic adjacent segment degeneration. The purpose of this study was to assess the pre-operative prevalence of adjacent segment degeneration in patients undergoing ACDF. A database review of three surgeons' practice was carried out to identify patients who had undergone a one- or two-level ACDF for degenerative disc disease. Patients were excluded if they were operated on for recent trauma, had an inflammatory arthropathy (for example, rheumatoid arthritis), or had previous spine surgery. The pre-operative MRI of each patient was reviewed and graded using a standardised methodology. One hundred and six patient MRI studies were reviewed. All patients showed some evidence of intervertebral disc degeneration adjacent to the planned operative segment(s). Increased severity of disc degeneration was associated with increased age and operative level, but was not associated with sagittal alignment. Disc degeneration was more common at levels adjacent to the surgical level than at non-adjacent segments, and was more severe at the superior adjacent level compared with the inferior adjacent level. These findings support the theory that adjacent segment degeneration following ACDF is due in part to the natural history of cervical spondylosis.

  6. Seasonal changes in phytoplankton biomass and dominant species in the Changjiang River Estuary and adjacent seas: General trends based on field survey data 1959-2009

    NASA Astrophysics Data System (ADS)

    Yang, Shu; Han, Xiurong; Zhang, Chuansong; Sun, Baiye; Wang, Xiulin; Shi, Xiaoyong

    2014-12-01

    The characteristics of seasonal variation in phytoplankton biomass and dominant species in the Changjiang River Estuary and adjacent seas were discussed based on field investigation data from 1959 to 2009. The field data from 1981 to 2004 showed that the Chlorophyll- a concentration in surface seawater was between 0.4 and 8.5 μg dm-3. The seasonal changes generally presented a bimodal trend, with the biomass peaks occurring in May and August, and Chlorophyll-a concentration was the lowest in winter. Seasonal biomass changes were mainly controlled by temperature and nutrient levels. From the end of autumn to the next early spring, phytoplankton biomass was mainly influenced by temperature, and in other seasons, nutrient level (including the nutrient supply from the terrestrial runoffs) was the major influence factor. Field investigation data from 1959 to 2009 demonstrated that diatoms were the main phytoplankton in this area, and Skeletonema costatum, Pseudo-nitzschia pungens, Coscinodiscus oculus-iridis, Thalassinoema nitzschioides, Paralia sulcata, Chaetoceros lorenzianus, Chaetoceros curvisetus, and Prorocentrum donghaiense Lu were common dominant species. The seasonal variations in major dominant phytoplankton species presented the following trends: 1) Skeletonema (mainly S. costatum) was dominant throughout the year; and 2) seasonal succession trends were Coscinodiscus (spring) → Chaetoceros (summer and autumn) → Coscinodiscus (winter). The annual dominance of S. costatum was attributed to its environmental eurytopicity and long standing time in surface waters. The seasonal succession of Coscinodiscus and Chaetoceros was associated with the seasonal variation in water stability and nutrient level in this area. On the other hand, long-term field data also indicated obvious interannual variation of phytoplankton biomass and community structure in the Changjiang River Estuary and adjacent seas: average annual phytoplankton biomass and dinoflagellate

  7. X-ray Pair Distribution Function Analysis of Potassium Based Geopolymer

    SciTech Connect

    Bell, J.; Sarin, P; Driemeyer, P; Haggerty, R; Chupas, P; Kriven, W

    2008-01-01

    The atomic structure of geopolymers is often described as amorphous with a local structure that is equivalent to that of crystalline zeolites. However, this structural relationship has never been quantified beyond a first-nearest-neighbor bonding environment. In this study, the short to medium range (1 nm) structural order of metakaolin-based KAlSi{sub 2}O{sub 6}{center_dot}5.5H{sub 2}O geopolymer was quantified and compared to zeolitic tetragonal leucite (KAlSi2O6) using the X-ray atomic pair distribution function technique. Unheated KAlSi{sub 2}O{sub 6}{center_dot}5.5H{sub 2}O was found to be structurally similar to leucite out to a length of 8 {angstrom}, but had increased medium range disorder over the 4.5 {angstrom} < r < 8 {angstrom} range. On heating to >300 C, changes in the short to medium range structure were observed due to dehydration and removal of chemically bound water. Crystallization of leucite occurred in samples heated beyond 1050 C. Refinements of a leucite model against the PDF data for geopolymer heated to 1100 C for 24 h yielded a good fit.

  8. An operationally flexible fuel cell based on quaternary ammonium-biphosphate ion pairs

    NASA Astrophysics Data System (ADS)

    Lee, Kwan-Soo; Spendelow, Jacob S.; Choe, Yoong-Kee; Fujimoto, Cy; Kim, Yu Seung

    2016-09-01

    Fuel cells are promising devices for clean power generation in a variety of economically and environmentally significant applications. Low-temperature proton exchange membrane (PEM) fuel cells utilizing Nafion require a high level of hydration, which limits the operating temperature to less than 100 ∘C. In contrast, high-temperature PEM fuel cells utilizing phosphoric acid-doped polybenzimidazole can operate effectively up to 180 ∘C however, these devices degrade when exposed to water below 140 ∘C. Here we present a different class of PEM fuel cells based on quaternary ammonium-biphosphate ion pairs that can operate under conditions unattainable with existing fuel cell technologies. These fuel cells exhibit stable performance at 80–160 ∘C with a conductivity decay rate more than three orders of magnitude lower than that of a commercial high-temperature PEM fuel cell. By increasing the operational flexibility, this class of fuel cell can simplify the requirements for heat and water management, and potentially reduce the costs associated with the existing fully functional fuel cell systems.

  9. Paired-Associate and Feedback-Based Weather Prediction Tasks Support Multiple Category Learning Systems

    PubMed Central

    Li, Kaiyun; Fu, Qiufang; Sun, Xunwei; Zhou, Xiaoyan; Fu, Xiaolan

    2016-01-01

    It remains unclear whether probabilistic category learning in the feedback-based weather prediction task (FB-WPT) can be mediated by a non-declarative or procedural learning system. To address this issue, we compared the effects of training time and verbal working memory, which influence the declarative learning system but not the non-declarative learning system, in the FB and paired-associate (PA) WPTs, as the PA task recruits a declarative learning system. The results of Experiment 1 showed that the optimal accuracy in the PA condition was significantly decreased when the training time was reduced from 7 to 3 s, but this did not occur in the FB condition, although shortened training time impaired the acquisition of explicit knowledge in both conditions. The results of Experiment 2 showed that the concurrent working memory task impaired the optimal accuracy and the acquisition of explicit knowledge in the PA condition but did not influence the optimal accuracy or the acquisition of self-insight knowledge in the FB condition. The apparent dissociation results between the FB and PA conditions suggested that a non-declarative or procedural learning system is involved in the FB-WPT and provided new evidence for the multiple-systems theory of human category learning. PMID:27445958

  10. The Common Prescription Patterns Based on the Hierarchical Clustering of Herb-Pairs Efficacies.

    PubMed

    Cao, Jia

    2016-01-01

    Prescription patterns are rules or regularities used to generate, recognize, or judge a prescription. Most of existing studies focused on the specific prescription patterns for diverse diseases or syndromes, while little attention was paid to the common patterns, which reflect the global view of the regularities of prescriptions. In this paper, we designed a method CPPM to find the common prescription patterns. The CPPM is based on the hierarchical clustering of herb-pair efficacies (HPEs). Firstly, HPEs were hierarchically clustered; secondly, the individual herbs are labeled by the HPEC (the clusters of HPEs); and then the prescription patterns were extracted from the combinations of HPEC; finally the common patterns are recognized statistically. The results showed that HPEs have hierarchical clustering structure. When the clustering level is 2 and the HPEs were classified into two clusters, the common prescription patterns are obvious. Among 332 candidate prescriptions, 319 prescriptions follow the common patterns. The description of the patterns is that if a prescription contains the herbs of the cluster (C 1), it is very likely to have other herbs of another cluster (C 2); while a prescription has the herbs of C 2, it may have no herbs of C 1. Finally, we discussed that the common patterns are mathematically coincident with the Blood-Qi theory.

  11. Paired-Associate and Feedback-Based Weather Prediction Tasks Support Multiple Category Learning Systems.

    PubMed

    Li, Kaiyun; Fu, Qiufang; Sun, Xunwei; Zhou, Xiaoyan; Fu, Xiaolan

    2016-01-01

    It remains unclear whether probabilistic category learning in the feedback-based weather prediction task (FB-WPT) can be mediated by a non-declarative or procedural learning system. To address this issue, we compared the effects of training time and verbal working memory, which influence the declarative learning system but not the non-declarative learning system, in the FB and paired-associate (PA) WPTs, as the PA task recruits a declarative learning system. The results of Experiment 1 showed that the optimal accuracy in the PA condition was significantly decreased when the training time was reduced from 7 to 3 s, but this did not occur in the FB condition, although shortened training time impaired the acquisition of explicit knowledge in both conditions. The results of Experiment 2 showed that the concurrent working memory task impaired the optimal accuracy and the acquisition of explicit knowledge in the PA condition but did not influence the optimal accuracy or the acquisition of self-insight knowledge in the FB condition. The apparent dissociation results between the FB and PA conditions suggested that a non-declarative or procedural learning system is involved in the FB-WPT and provided new evidence for the multiple-systems theory of human category learning.

  12. Paired-Associate and Feedback-Based Weather Prediction Tasks Support Multiple Category Learning Systems.

    PubMed

    Li, Kaiyun; Fu, Qiufang; Sun, Xunwei; Zhou, Xiaoyan; Fu, Xiaolan

    2016-01-01

    It remains unclear whether probabilistic category learning in the feedback-based weather prediction task (FB-WPT) can be mediated by a non-declarative or procedural learning system. To address this issue, we compared the effects of training time and verbal working memory, which influence the declarative learning system but not the non-declarative learning system, in the FB and paired-associate (PA) WPTs, as the PA task recruits a declarative learning system. The results of Experiment 1 showed that the optimal accuracy in the PA condition was significantly decreased when the training time was reduced from 7 to 3 s, but this did not occur in the FB condition, although shortened training time impaired the acquisition of explicit knowledge in both conditions. The results of Experiment 2 showed that the concurrent working memory task impaired the optimal accuracy and the acquisition of explicit knowledge in the PA condition but did not influence the optimal accuracy or the acquisition of self-insight knowledge in the FB condition. The apparent dissociation results between the FB and PA conditions suggested that a non-declarative or procedural learning system is involved in the FB-WPT and provided new evidence for the multiple-systems theory of human category learning. PMID:27445958

  13. Heterochromatin base pair composition and diversification in holocentric chromosomes of kissing bugs (Hemiptera, Reduviidae)

    PubMed Central

    Bardella, Vanessa Bellini; Pita, Sebastián; Vanzela, André Luis Laforga; Galvão, Cleber; Panzera, Francisco

    2016-01-01

    The subfamily Triatominae (Hemiptera, Reduviidae) includes 150 species of blood-sucking insects, vectors of Chagas disease or American trypanosomiasis. Karyotypic information reveals a striking stability in the number of autosomes. However, this group shows substantial variability in genome size, the amount and distribution of C-heterochromatin, and the chromosome positions of 45S rDNA clusters. Here, we analysed the karyotypes of 41 species from six different genera with C-fluorescence banding in order to evaluate the base-pair richness of heterochromatic regions. Our results show a high heterogeneity in the fluorescent staining of the heterochromatin in both autosomes and sex chromosomes, never reported before within an insect subfamily with holocentric chromosomes. This technique allows a clear discrimination of the heterochromatic regions classified as similar by C-banding, constituting a new chromosome marker with taxonomic and evolutionary significance. The diverse fluorescent patterns are likely due to the amplification of different repeated sequences, reflecting an unusual dynamic rearrangement in the genomes of this subfamily. Further, we discuss the evolution of these repeated sequences in both autosomes and sex chromosomes in species of Triatominae. PMID:27759763

  14. Simplified Aircraft-Based Paired Approach: Concept Definition and Initial Analysis

    NASA Technical Reports Server (NTRS)

    Johnson, Sally C.; Lohr, Gary W.; McKissick, Burnell T.; Abbott, Terence S.; Geurreiro, Nelson M.; Volk, Paul

    2013-01-01

    Simplified Aircraft-based Parallel Approach (SAPA) is an advanced concept proposed by the Federal Aviation Administration (FAA) to support dependent parallel approach operations to runways with lateral spacing closer than 2500 ft. At the request of the FAA, NASA performed an initial assessment of the potential performance and feasibility of the SAPA concept, including developing and assessing an operational implementation of the concept and conducting a Monte Carlo wake simulation study to examine the longitudinal spacing requirements. The SAPA concept was shown to have significant operational advantages in supporting the pairing of aircraft with dissimilar final approach speeds. The wake simulation study showed that support for dissimilar final approach speeds could be significantly enhanced through the use of a two-phased altitudebased longitudinal positioning requirement, with larger longitudinal positioning allowed for higher altitudes out of ground effect and tighter longitudinal positioning defined for altitudes near and in ground effect. While this assessment is preliminary and there are a number of operational issues still to be examined, it has shown the basic SAPA concept to be technically and operationally feasible.

  15. An operationally flexible fuel cell based on quaternary ammonium-biphosphate ion pairs

    DOE PAGES

    Lee, Kwan -Soo; Spendelow, Jacob Schatz; Choe, Yoong -Kee; Fujimoto, Cy; Kim, Yu Seung

    2016-08-22

    Here, fuel cells are promising devices for clean power generation in a variety of economically and environmentally significant applications. Low-temperature proton exchange membrane (PEM) fuel cells utilizing Nafion require a high level of hydration, which limits the operating temperature to less than 100°C. In contrast, high-temperature PEM fuel cells utilizing phosphoric acid-doped polybenzimidazole can operate effectively up to 180°C; however, these devices degrade when exposed to water below 140°C. Here we present a different class of PEM fuel cells based on quaternary ammonium-biphosphate ion pairs that can operate under conditions unattainable with existing fuel cell technologies. These fuel cells exhibitmore » stable performance at 80–160°C with a conductivity decay rate more than three orders of magnitude lower than that of a commercial high-temperature PEM fuel cell. By increasing the operational flexibility, this class of fuel cell can simplify the requirements for heat and water management, and potentially reduce the costs associated with the existing fully functional fuel cell systems.« less

  16. An operationally flexible fuel cell based on quaternary ammonium-biphosphate ion pairs

    NASA Astrophysics Data System (ADS)

    Lee, Kwan-Soo; Spendelow, Jacob S.; Choe, Yoong-Kee; Fujimoto, Cy; Kim, Yu Seung

    2016-09-01

    Fuel cells are promising devices for clean power generation in a variety of economically and environmentally significant applications. Low-temperature proton exchange membrane (PEM) fuel cells utilizing Nafion require a high level of hydration, which limits the operating temperature to less than 100 ∘C. In contrast, high-temperature PEM fuel cells utilizing phosphoric acid-doped polybenzimidazole can operate effectively up to 180 ∘C however, these devices degrade when exposed to water below 140 ∘C. Here we present a different class of PEM fuel cells based on quaternary ammonium-biphosphate ion pairs that can operate under conditions unattainable with existing fuel cell technologies. These fuel cells exhibit stable performance at 80-160 ∘C with a conductivity decay rate more than three orders of magnitude lower than that of a commercial high-temperature PEM fuel cell. By increasing the operational flexibility, this class of fuel cell can simplify the requirements for heat and water management, and potentially reduce the costs associated with the existing fully functional fuel cell systems.

  17. Simulation Based on Ion Propulsion Rocket System with Using Negative ion - Negative Ion Pair Techniques

    NASA Astrophysics Data System (ADS)

    Sathiyavel, C.

    2016-07-01

    Ion propulsion rocket system is expected to become popular with the development of ion-ion pair techniques because of their stimulated of low propellant, Design of Thrust range is 1N with low electric power and high efficiency. A Negative ion-Negative ion pair of ion propulsion rocket system is proposed in this work .Negative Ion Based Rocket system consists of three parts 1.ionization chamber 2. Repulsion force and ion accelerator 3. Exhaust of Nozzle. The Negative ions from electro negatively gas are produced by attachment of the gas ,such as chlorine with electron emitted from a Electron gun ionization chamber. The formulate of large stable negative ion is achievable in chlorine gas with respect to electron affinity (∆E). The electron affinity is a measure of the energy change when an electron is added to a neutral atom to form a negative ion. When a neutral chlorine atom in the gaseous form picks up an electron to form a Cl- ion, it releases energy of 349 kJ/mol or 3.6 ev/atom. It is said to have an electron affinity of -349 kJ/mol ,the negative sign indicating that energy is released during this process .The mechanisms of attachment involve the formation of intermediate states. In that reason for , the highly repulsive force created between the same negative ions. The distance between same negative ions is important for the evaluate of the rocket thrust and is also determined by the exhaust velocity of the propellant. The mass flow rate of propellant is achieved by the ratio of total mass of the propellant (Kg) needed for operation to time period(s). Accelerate the Negative ions to a high velocity in the thrust vector direction with a significantly intense Magnetic field and the exhaust of negative ions through Nozzle. The simulation of the ion propulsion system has been carried out by MATLAB. By comparing the simulation results with the theoretical and previous results, we have found that the proposed method is achieved of thrust value with estimated

  18. Universal quantum gates for Single Cooper Pair Box based quantum computing

    NASA Technical Reports Server (NTRS)

    Echternach, P.; Williams, C. P.; Dultz, S. C.; Braunstein, S.; Dowling, J. P.

    2000-01-01

    We describe a method for achieving arbitrary 1-qubit gates and controlled-NOT gates within the context of the Single Cooper Pair Box (SCB) approach to quantum computing. Such gates are sufficient to support universal quantum computation.

  19. System for DNA sequencing with resolution of up to 600 base pairs.

    PubMed

    Ansorge, W; Barker, R

    1984-03-01

    A system capable of resolving about 500 bases is of interest for sequencing of longer DNA molecules. Studies on further optimization of resolution on DNA sequencing gels were carried out. The effect of physico-chemical properties of gels and buffers on resolution were tested, e.g. ionic strength and pH of buffers, different buffer systems, acrylamide concentration, crosslinker concentration, type of crosslinker, temperature of polymerization, denaturing conditions, gel length and thickness. Tested were as well different running conditions like electric field, gel temperature, dimension of sample slots. Gels 0.1-0.2 mm thick and up to 1.2 m long were cast and tested routinely. Gel lengths of 60-70 cm (for sequencing up to 350-400 bases) to about 100 cm (above 400 bases) are practicable. Little is gained in resolution by increasing the gel length from 1 to 1.2 m. Resolution was improved using 0.1 mm thick gels, at a higher pH value of 8.6-8.8, and molarity increased to 0.2 M. The sequencing pattern in the region of higher bases could be better resolved on a twice-magnified picture of that region on the autoradiogram. With the long gels (70-120 cm), it is advantageous to obtain the sequence overlap by running in parallel gels of different concentrations, without re-application of samples, all loaded at the same time. Buffer chamber for running of two of three gels and thermostating plates up to 1.2 m long were designed. In this way four to six thermostated gels can be run from a power supply with two inputs. Three 1 m long gels (concentrations: 4%, 6%, 12-16%) are loaded with several samples of DNA to be sequenced and run in parallel without re-application of the samples. With good samples, the sequence overlap from the gels could be counted up to 500 base pairs, with exceptionally good samples closer to 600 bases. At present this number seems to be near the limit of the resolving power of the polyacrylamide gels. PMID:6725850

  20. Metal-semiconductor pair nanoparticles by a physical route based on bipolar mixing.

    PubMed

    Kala, Shubhra; Theissmann, Ralf; Rouenhoff, Marcel; Kruis, Frank Einar

    2016-03-29

    In this report a methodology is described and demonstrated for preparing Au-Ge pair nanoparticles with known compositions by extending and modifying the basic steps normally used to synthesize nanoparticles in carrier gas. For the formation of pair nanoparticles by bipolar mixing, two oppositely charged aerosols of nanoparticles having the desired size are produced with the help of two differential mobility analyzers. Then both are allowed to pass through a tube, which provides sufficient residence time to result in nanoparticle pair formation due to Brownian collisions influenced by Coulomb forces. The effect of residence time on the formation of nanoparticle pairs as well as the influence of diffusion and discharging is described. Subsequently, necessary modifications to the experimental setup are demonstrated systematically. The kinetics of nanoparticles pair formation in a carrier gas is also calculated and compared with measurements made with the help of an online aerosol size analysis technique. This synthesis of nanoparticle pairs can be seen as a possible route towards Janus-type nanoparticles.

  1. Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs

    SciTech Connect

    Patra, Amritraj; Harp, Joel; Pallan, Pradeep S.; Zhao, Linlin; Abramov, Mikhail; Herdewijn, Piet; Egli, Martin

    2012-12-28

    The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marlière,P., Patrouix,J., Döring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium’s genome. Angew. Chem. Int. Ed., 50, 7109–7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T→ClU genome substitution.

  2. Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.

    PubMed Central

    Beuning, Penny J; Nagan, Maria C; Cramer, Christopher J; Musier-Forsyth, Karin; Gelpí, Josep-Lluis; Bashford, Donald

    2002-01-01

    Specific aminoacylation by aminoacyl-tRNA synthetases requires accurate recognition of cognate tRNA substrates. In the case of alanyl-tRNA synthetase (AlaRS), RNA duplexes that mimic the acceptor stem of the tRNA are efficient substrates for aminoacylation in vitro. It was previously shown that recognition by AlaRS is severely affected by a simple base pair transversion of the G2:C71 pair at the second position in the RNA helix. In this study, we determined the aminoacylation efficiencies of 50 variants of the tRNA(Ala) acceptor stem containing substitutions at the 2:71 position. We find that there is not a single functional group of the wild-type G2:C71 base pair that is critical for positive recognition. Rather, we observed that base-pair orientation plays an important role in recognition. In particular, pyrimidine2:purine71 combinations generally resulted in decreased aminoacylation efficiency compared to the corresponding purine:pyrimidine pair. Moreover, the activity of a pyrimidine:purine variant could be partially restored by the presence of a major groove amino group at position 71. In an attempt to understand this result further, dielectric continuum electrostatic calculations were carried out, in some cases with additional inclusion of van der Waals interaction energies, to determine interaction potentials of the wild-type duplexAla and seven 2:71 variants. This analysis revealed a positive correlation between major groove negative electrostatic potential in the vicinity of the 3:70 base pair and measured aminoacylation efficiency. PMID:12022232

  3. Photoinduced electron transfer in a Watson-Crick base-paired, 2-aminopurine:uracil-C60 hydrogen bonding conjugate.

    PubMed

    D'Souza, Francis; Gadde, Suresh; Islam, D-M Shafiqul; Pang, Siew-Cheng; Schumacher, Amy Lea; Zandler, Melvin E; Horie, Rumiko; Araki, Yasuyaki; Ito, Osamu

    2007-02-01

    A fluorescent reporter molecule, 2-aminopurine was self-assembled via Watson-Crick base-pairing to a uracil appended fullerene to form a donor-acceptor conjugate; efficient photoinduced charge separation was confirmed by time-resolved emission and transient absorption spectral studies.

  4. Relationship between the 19 base pair deletion polymorphism in DHFR and unmetabolized folic and in plasma and RBC folate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: A 19 base pair (bp) deletion allele of dihydrofolate reductase (DHFR), an enzyme that makes folic acid metabolically active and reduces dihydrofolate to tetrahydrofolate to stimulate folate turnover, has been implicated in folate related health outcomes. Objective: Examine the effect ...

  5. Transitions between Short-Term and Long-Term Memory in Learning Meaningful Unrelated Paired Associates Using Computer Based Drills.

    ERIC Educational Resources Information Center

    Goldenberg, Tzvika Y.; Turnure, James E.

    1989-01-01

    Discussion of short-term and long-term memory in learning paired associates focuses on two microcomputer-based instructional design experiments with eleventh and twelfth graders that were modeled after traditional drill and practice routines. Research questions are presented, treatment conditions are explained, and additional research is…

  6. The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs.

    PubMed

    Halder, Antarip; Bhattacharya, Sohini; Datta, Ayan; Bhattacharyya, Dhananjay; Mitra, Abhijit

    2015-10-21

    The roles of protonated nucleobases in stabilizing different structural motifs and in facilitating catalytic functions of RNA are well known. Among different polar sites of all the nucleobases, N7 of guanine has the highest protonation propensity at physiological pH. However, unlike other easily protonable sites such as N1 and N3 of adenine or N3 of cytosine, N7 protonation of guanine does not lead to the stabilization of base pairs involving its protonated Hoogsteen edge. It also does not facilitate its participation in any acid-base catalysis process. To explore the possible roles of N7 protonated guanine, we have studied its base pairing potentials involving WatsonCrick and sugar edges, which undergo major charge redistribution upon N7 protonation. We have carried out quantum chemical geometry optimization at the M05-2X/6-311G+(2d,2p) level, followed by interaction energy calculation at the MP2/aug-cc-pVDZ level, along with the analysis of the context of occurrence for selected base pairs involving the sugar edge or the WatsonCrick edge of guanine within a non-redundant set of 167 RNA crystal structures. Our results suggest that, four base pairs - G:C W:W trans, G:rC W:S cis, G:G W:H cis and G:G S:H trans may involve N7 protonated guanine. These base pairs deviate significantly from their respective experimental geometries upon QM optimization, but they retain their experimental geometries if guanine N7 protonation is considered during optimization. Our study also reveals the role of guanine N7 protonation (i) in stabilizing important RNA structural motifs, (ii) in providing a framework for designing pH driven molecular motors and (iii) in providing an alternative strategy to mimic the effect of post-transcriptional changes. PMID:26382322

  7. Breathing fluctuations in position-specific DNA base pairs are involved in regulating helicase movement into the replication fork.

    PubMed

    Jose, Davis; Weitzel, Steven E; von Hippel, Peter H

    2012-09-01

    We previously used changes in the near-UV circular dichroism and fluorescence spectra of DNA base analogue probes placed site specifically to show that the first three base pairs at the fork junction in model replication fork constructs are significantly opened by "breathing" fluctuations under physiological conditions. Here, we use these probes to provide mechanistic snapshots of the initial interactions of the DNA fork with a tight-binding replication helicase in solution. The primosome helicase of bacteriophage T4 was assembled from six (gp41) helicase subunits, one (gp61) primase subunit, and nonhydrolyzable GTPγS. When bound to a DNA replication fork construct this complex advances one base pair into the duplex portion of the fork and forms a stably bound helicase "initiation complex." Replacement of GTPγS with GTP permits the completion of the helicase-driven unwinding process. Our spectroscopic probes show that the primosome in this stable helicase initiation complex binds the DNA of the fork primarily via backbone contacts and holds the first complementary base pair of the fork in an open conformation, whereas the second, third, and fourth base pairs of the duplex show essentially the breathing behavior that previously characterized the first three base pairs of the free fork. These spectral changes, together with dynamic fluorescence quenching results, are consistent with a primosome-binding model in which the lagging DNA strand passes through the central hole of the hexagonal helicase, the leading strand binds to the "outside" surfaces of subunits of the helicase hexamer, and the single primase subunit interacts with both strands.

  8. Computer simulation of acetonitrile and methanol with ab initio-based pair potentials

    NASA Astrophysics Data System (ADS)

    Hloucha, M.; Sum, A. K.; Sandler, S. I.

    2000-10-01

    This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.

  9. Comparison of Three Cre-LoxP Based Paired-End Library Construction Methods

    SciTech Connect

    Peng, Ze; Nath, Nandita; Tritt, Andrew; Liang, Shoudan; Han, James; Pennacchio, Len; Chen, Feng

    2013-03-26

    Paired-end library sequencing has been proven useful in scaffold construction during de novo whole genome shotgun assembly. The ability of generating mate pairs with > 8 Kb insert sizes is especially important for genomes containing long repeats. To make mate paired libraries for next generation sequencing, DNA fragments need to be circularized to bring the ends together. There are several methods that can be used for DNA circulation, namely ligation, hybridization and Cre-LoxP recombination. With higher circularization efficiency with large insert DNA fragments, Cre-LoxP recombination method generally has been used for constructing >8 kb insert size paired-end libraries. Second fragmentation step is also crucial for maintaining high library complexity and uniform genome coverage. Here we will describe the following three fragmentation methods: restriction enzyme digestion, random shearing and nick translation. We will present the comparison results for these three methods. Our data showed that all three methods are able to generate paired-end libraries with greater than 20 kb insert. Advantages and disadvantages of these three methods will be discussed as well.

  10. Mitochondrial DNA 4977-base pair common deletion in blood leukocytes and melanoma risk.

    PubMed

    Shen, Jie; Wan, Jie; Huff, Chad; Fang, Shenying; Lee, Jeffrey E; Zhao, Hua

    2016-05-01

    The 4977-base pair common deletion DmtDNA4977 is the most frequently observed mitochondrial DNA mutation in human tissues. Because mitochondrial DNA mutations are mainly caused by reactive oxygen species (ROS), and given that oxidative stress plays an important role in melanoma carcinogenesis, the investigation of DmtDNA4977 may be particularly relevant to the development of melanoma. In this study, we compared DmtDNA4977 levels in blood leukocytes from 206 melanoma patients and 219 healthy controls. Overall, melanoma cases had significantly higher levels of DmtDNA4977 than healthy controls (median: 0.60 vs 0.20, P = 0.008). The difference was evident among individuals who were older than 47 yrs, women, and had pigmentation risk factors (e.g., blond or red hair, blue eye, fair skin, light, or none tanning ability after prolonged sun exposure, and freckling in the sun as a child). The difference was also evident among those who had at least one lifetime sunburn with blistering and had no reported use of a sunlamp. Interestingly, among controls, DmtDNA4977 levels differed by phenotypic index and reported use of a sunlamp. In the risk assessment, increased levels of DmtDNA4977 were associated with a 1.23-fold increased risk of melanoma (odds ratio (OR): 1.23, 95% confidence interval (90% CI): 1.01, 1.50). A significant dose-response relationship was observed in quartile analysis (P = 0.001). In summary, our study suggests that high levels of DmtDNA4977 in blood leukocytes are associated with increased risk of melanoma and that association is affected by both pigmentation and personal history of sun exposure. PMID:26988264

  11. Base pair sensitivity and enhanced ON/OFF ratios of DNA-binding: donor-acceptor-donor fluorophores.

    PubMed

    Wilson, James N; Wigenius, Jens; Pitter, Demar R G; Qiu, Yanhua; Abrahamsson, Maria; Westerlund, Fredrik

    2013-10-10

    The photophysical properties of two recently reported live cell compatible, DNA-binding dyes, 4,6-bis(4-(4-methylpiperazin-1-yl)phenyl)pyrimidin-2-ol, 1, and [1,3-bis[4-(4-methylpiperazin-1-yl)phenyl]-1,3-propandioato-κO, κO']difluoroboron, 2, are characterized. Both dyes are quenched in aqueous solutions, while binding to sequences containing only AT pairs enhances the emission. Binding of the dyes to sequences containing only GC pairs does not produce a significant emission enhancement, and for sequences containing both AT and GC base pairs, emission is dependent on the length of the AT pair tracts. Through emission lifetime measurements and analysis of the dye redox potentials, photoinduced electron transfer with GC pairs is implicated as a quenching mechanism. Binding of the dyes to AT-rich regions is accompanied by bathochromic shifts of 26 and 30 nm, respectively. Excitation at longer wavelengths thus increases the ON/OFF ratio of the bound probes significantly and provides improved contrast ratios in solution as well as in fluorescence microscopy of living cells. PMID:24079271

  12. A terrain-based paired-site sampling design to assess biodiversity losses from eastern hemlock decline

    USGS Publications Warehouse

    Young, J.A.; Smith, D.R.; Snyder, C.D.; Lemarie, D.P.

    2002-01-01

    Biodiversity surveys are often hampered by the inability to control extraneous sources of variability introduced into comparisons of populations across a heterogenous landscape. If not specifically accounted for a priori, this noise can weaken comparisons between sites, and can make it difficult to draw inferences about specific ecological processes. We developed a terrain-based, paired-site sampling design to analyze differences in aquatic biodiversity between streams draining eastern hemlock (Tsuga canadensis) forests, and those draining mixed hardwood forests in Delaware Water Gap National Recreation Area (USA). The goal of this design was to minimize variance due to terrain influences on stream communities, while representing the range of hemlock dominated stream environments present in the park. We used geographic information systems (GIS) and cluster analysis to define and partition hemlock dominated streams into terrain types based on topographic variables and stream order. We computed similarity of forest stands within terrain types and used this information to pair hemlock-dominated streams with hardwood counterparts prior to sampling. We evaluated the effectiveness of the design through power analysis and found that power to detect differences in aquatic invertebrate taxa richness was highest when sites were paired and terrain type was included as a factor in the analysis. Precision of the estimated difference in mean richness was nearly doubled using the terrain-based, paired site design in comparison to other evaluated designs. Use of this method allowed us to sample stream communities representative of park-wide forest conditions while effectively controlling for landscape variability.

  13. Ion-pair association and acid-base equilibria in nonaqueous capillary electrophoresis of weakly basic compounds.

    PubMed

    Carabias-Martínez, Rita; Rodríguez-Gonzalo, Encarnación; Hernández-Méndez, Jesús; Cruz, Edith Miranda; Domínguez-Alvarez, Javier

    2006-02-01

    CE in nonaqueous media was used to study the migrating behavior of two weakly basic s-triazine pesticides and one of their metabolites. The target pesticides were selected to be representative for each of the two main groups: propazine and deethylatrazine for the chloro-s-triazines group and ametryn for the methylthio-s-triazines group. To elucidate the phenomena involved, systematic studies were carried out in the different organic media studied. Absolute mobilities were determined in 50% v/v methanol (MeOH)/ACN by extrapolation of the effective mobilities to zero ionic strength in the presence of different concentrations of perchloric acid. Conductivity measurements performed in MeOH and 50 and 20% v/v methanol/ACN permitted the evaluation of the associations of the components of the BGE. The effects of ionic strength on the actual mobilities of the compounds were determined in the presence of perchloric acid and SDS in different organic media. Two different ion-pair equilibria were considered: one due to the presence of perchlorate anions present in the BGE and second that from the added dodecyl sulfate anions. Bearing in mind that these weakly basic compounds can exhibit ion-pair and acid-base equilibria, the acid-base and ion-pair parasite reaction coefficients were determined. Finally, the effects of ionic strength, ion-pair interactions and acid-base properties on the effective electrophoretic mobilities of the analytes are discussed.

  14. New Chemometrics Mode Based on Adjacent Data Points’ Differences for the Simultaneous Determination of Clopidogrel, Atorvastatin, and Aspirin in their Combined Ternary Drug Formulation

    PubMed Central

    Nejem, R’afat Mahmoud; Issa, Mahmoud Mohamed; Shanab, Alaa Abu; Stefan-Van Staden, Raluca-Ioana; Aboul-Enein, Hassan Y.

    2014-01-01

    Abstract A new method is proposed for the analysis of a ternary mixture composed of clopidogrel, atorvastatin, and aspirin without prior separation steps. The method combines the advantages of the mean centering of ratio spectra and derivative spectrophotometric methods. It is based on using the difference between adjacent data points in the absorbance spectra. The principal advantage of this method is the use of absorbance data, and not derivative data; hence the signal-to-noise ratio is not diminished. The mathematical explanation of the procedure is illustrated. Beer’s law was valid in the concentration range 0.3–35 μg.mL-1 for CLOP, 0.5–30 μg.mL-1 for ATOR, and 1–40 μg.mL-1 for ASP. Mean recoveries were obtained as 100.2, 100.1, and 100.2% for CLOP, ATOR, and ASP, respectively, in the prepared synthetic mixtures. The method has been successfully applied to the simultaneous determination of ternary mixtures of aspirin, clopidogrel bisulphate, and atorvastatin calcium. The analytical characteristics of the method were calculated. The results showed that the new method is simple, rapid, accurate, and precise. PMID:25853071

  15. 1,8-Naphthyridine-2,7-diamine: A Potential Universal Reader of the Watson-Crick Base Pairs for DNA Sequencing by Electron Tunneling

    PubMed Central

    Liang, Feng; Lindsay, Stuart; Zhang, Peiming

    2013-01-01

    With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read the DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A:T and G:C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs. PMID:23038027

  16. Adjusted Wald Confidence Interval for a Difference of Binomial Proportions Based on Paired Data

    ERIC Educational Resources Information Center

    Bonett, Douglas G.; Price, Robert M.

    2012-01-01

    Adjusted Wald intervals for binomial proportions in one-sample and two-sample designs have been shown to perform about as well as the best available methods. The adjusted Wald intervals are easy to compute and have been incorporated into introductory statistics courses. An adjusted Wald interval for paired binomial proportions is proposed here and…

  17. Paired Learners' Verbalised Strategies for Determining Grammatical Correctness: A Turn-Based System for Coding Metatalk

    ERIC Educational Resources Information Center

    Ishii, David N.

    2011-01-01

    The purpose of this paper is to explore the use of a new coding system that incorporates the various types of metatalk that occurred during paired learners' engagement in a consciousness-raising task. On the basis of previous studies, metalanguage (e.g. with or without terminology), knowledge sources (e.g. intuition), and verbalisation strategies…

  18. Contact ion pair formation between hard acids and soft bases in aqueous solutions observed with 2DIR spectroscopy.

    PubMed

    Sun, Zheng; Zhang, Wenkai; Ji, Minbiao; Hartsock, Robert; Gaffney, Kelly J

    2013-12-12

    The interaction of charged species in aqueous solution has important implications for chemical, biological, and environmental processes. We have used 2DIR spectroscopy to study the equilibrium dynamics of thiocyanate chemical exchange between free ion (NCS(-)) and contact ion pair configurations (MNCS(+)), where M(2+) = Mg(2+) or Ca(2+). Detailed studies of the influence of anion concentration and anion speciation show that the chemical exchange observed with the 2DIR measurements results from NCS(-) exchanging with other anion species in the first solvation shell surrounding Mg(2+) or Ca(2+). The presence of chemical exchange in the 2DIR spectra provides an indirect, but robust, determinant of contact ion pair formation. We observe preferential contact ion pair formation between soft Lewis base anions and hard Lewis acid cations. This observation cannot be easily reconciled with Pearson's acid-base concept or Collins' Law of Matching Water Affinities. The anions that form contact ion pairs also correspond to the ions with an affinity for water and protein surfaces, so similar physical and chemical properties may control these distinct phenomena. PMID:23895531

  19. Contact ion pair formation between hard acids and soft bases in aqueous solutions observed with 2DIR spectroscopy.

    PubMed

    Sun, Zheng; Zhang, Wenkai; Ji, Minbiao; Hartsock, Robert; Gaffney, Kelly J

    2013-12-12

    The interaction of charged species in aqueous solution has important implications for chemical, biological, and environmental processes. We have used 2DIR spectroscopy to study the equilibrium dynamics of thiocyanate chemical exchange between free ion (NCS(-)) and contact ion pair configurations (MNCS(+)), where M(2+) = Mg(2+) or Ca(2+). Detailed studies of the influence of anion concentration and anion speciation show that the chemical exchange observed with the 2DIR measurements results from NCS(-) exchanging with other anion species in the first solvation shell surrounding Mg(2+) or Ca(2+). The presence of chemical exchange in the 2DIR spectra provides an indirect, but robust, determinant of contact ion pair formation. We observe preferential contact ion pair formation between soft Lewis base anions and hard Lewis acid cations. This observation cannot be easily reconciled with Pearson's acid-base concept or Collins' Law of Matching Water Affinities. The anions that form contact ion pairs also correspond to the ions with an affinity for water and protein surfaces, so similar physical and chemical properties may control these distinct phenomena.

  20. Intense charge transfer surface based on graphene and thymine-Hg(II)-thymine base pairs for detection of Hg(2.).

    PubMed

    Li, Jiao; Lu, Liping; Kang, Tianfang; Cheng, Shuiyuan

    2016-03-15

    In this article, we developed an electrochemiluminescence (ECL) sensor with a high-intensity charge transfer interface for Hg(2+) detection based on Hg(II)-induced DNA hybridization. The sensor was fabricated by the following simple method. First, graphene oxide (GO) was electrochemically reduced onto a glassy carbon electrode through cyclic voltammetry. Then, amino-labeled double-stranded (ds)DNA was assembled on the electrode surface using 1-pyrenebutyric acid N-hydroxysuccinimide as a linker between GO and DNA. The other terminal of dsDNA, which was labeled with biotin, was linked to CdSe quantum dots via biotin-avidin interactions. Reduced graphene oxide has excellent electrical conductivity. dsDNA with T-Hg(II)-T base pairs exhibited more facile charge transfer. They both accelerate the electron transfer performance and sensitivity of the sensor. The increased ECL signals were logarithmically linear with the concentration of Hg(II) when Hg(2+) was present in the detection solution. The linear range of the sensor was 10(-11) to 10(-8)mol/L (R=0.9819) with a detection limit of 10(-11)mol/L. This biosensor exhibited satisfactory results when it was used to detect Hg(II) in real water samples. The biosensor with high-intense charge transfer performance is a prospect avenue to pursue more and more sensitive detection method. PMID:26499870

  1. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function

    PubMed Central

    Huang, Lin; Wang, Jia; Lilley, David M. J.

    2016-01-01

    k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G•A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures. PMID:27016741

  2. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function.

    PubMed

    Huang, Lin; Wang, Jia; Lilley, David M J

    2016-06-20

    k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G•A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures. PMID:27016741

  3. Development of a clinician reputation metric to identify appropriate problem-medication pairs in a crowdsourced knowledge base

    PubMed Central

    McCoy, Allison B.; Wright, Adam; Rogith, Deevakar; Fathiamini, Safa; Ottenbacher, Allison J.; Sittig, Dean F.

    2014-01-01

    Background Correlation of data within electronic health records is necessary for implementation of various clinical decision support functions, including patient summarization. A key type of correlation is linking medications to clinical problems; while some databases of problem-medication links are available, they are not robust and depend on problems and medications being encoded in particular terminologies. Crowdsourcing represents one approach to generating robust knowledge bases across a variety of terminologies, but more sophisticated approaches are necessary to improve accuracy and reduce manual data review requirements. Objective We sought to develop and evaluate a clinician reputation metric to facilitate the identification of appropriate problem-medication pairs through crowdsourcing without requiring extensive manual review. Approach We retrieved medications from our clinical data warehouse that had been prescribed and manually linked to one or more problems by clinicians during e-prescribing between June 1, 2010 and May 31, 2011. We identified measures likely to be associated with the percentage of accurate problem-medication links made by clinicians. Using logistic regression, we created a metric for identifying clinicians who had made greater than or equal to 95% appropriate links. We evaluated the accuracy of the approach by comparing links made by those physicians identified as having appropriate links to a previously manually validated subset of problem-medication pairs. Results Of 867 clinicians who asserted a total of 237,748 problem-medication links during the study period, 125 had a reputation metric that predicted the percentage of appropriate links greater than or equal to 95%. These clinicians asserted a total of 2464 linked problem-medication pairs (983 distinct pairs). Compared to a previously validated set of problem-medication pairs, the reputation metric achieved a specificity of 99.5% and marginally improved the sensitivity of

  4. A model for 3:2 HFQPO pairs in black hole binaries based on cosmic battery

    NASA Astrophysics Data System (ADS)

    Huang, Chang-Yin; Ye, Yong-Chun; Wang, Ding-Xiong; Li, Yang

    2016-04-01

    A model for 3:2 high-frequency quasi-periodic oscillations (HFQPOs) with 3:2 pairs observed in four black hole X-ray binaries (BHXBs) is proposed by invoking the epicyclic resonances with the magnetic connection (MC) between a spinning black hole (BH) with a relativistic accretion disc. It turns out that the MC can be worked out due to Poynting-Robertson cosmic battery, and the 3:2 HFQPO pairs associated with the steep power-law states can be fitted in this model. Furthermore, the severe damping problem in the epicyclic resonance model can be overcome by transferring energy from the BH to the inner disc via the MC process for emitting X-rays with sufficient amplitude and coherence to produce the HFQPOs. In addition, we discuss the important role of the magnetic field in state transition of BHXBs.

  5. Transition state in DNA polymerase β catalysis: rate-limiting chemistry altered by base-pair configuration.

    PubMed

    Oertell, Keriann; Chamberlain, Brian T; Wu, Yue; Ferri, Elena; Kashemirov, Boris A; Beard, William A; Wilson, Samuel H; McKenna, Charles E; Goodman, Myron F

    2014-03-25

    Kinetics studies of dNTP analogues having pyrophosphate-mimicking β,γ-pCXYp leaving groups with variable X and Y substitution reveal striking differences in the chemical transition-state energy for DNA polymerase β that depend on all aspects of base-pairing configurations, including whether the incoming dNTP is a purine or pyrimidine and if base-pairings are right (T•A and G•C) or wrong (T•G and G•T). Brønsted plots of the catalytic rate constant (log(kpol)) versus pKa4 for the leaving group exhibit linear free energy relationships (LFERs) with negative slopes ranging from -0.6 to -2.0, consistent with chemical rate-determining transition-states in which the active-site adjusts to charge-stabilization demand during chemistry depending on base-pair configuration. The Brønsted slopes as well as the intercepts differ dramatically and provide the first direct evidence that dNTP base recognition by the enzyme-primer-template complex triggers a conformational change in the catalytic region of the active-site that significantly modifies the rate-determining chemical step. PMID:24580380

  6. Modeling and optimization of photon pair sources based on spontaneous parametric down-conversion

    SciTech Connect

    Kolenderski, Piotr; Banaszek, Konrad; Wasilewski, Wojciech

    2009-07-15

    We address the problem of efficient modeling of photon pairs generated in spontaneous parametric down-conversion and coupled into single-mode fibers. It is shown that when the range of relevant transverse wave vectors is restricted by the pump and fiber modes, the computational complexity can be reduced substantially with the help of the paraxial approximation, while retaining the full spectral characteristics of the source. This approach can serve as a basis for efficient numerical calculations or can be combined with analytically tractable approximations of the phase-matching function. We introduce here a cosine-Gaussian approximation of the phase-matching function that works for a broader range of parameters than the Gaussian model used previously. The developed modeling tools are used to evaluate characteristics of the photon pair sources such as the pair production rate and the spectral purity quantifying frequency correlations. Strategies to generate spectrally uncorrelated photons, necessary in multiphoton interference experiments, are analyzed with respect to trade-offs between parameters of the source.

  7. 2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes

    PubMed Central

    Sochacka, Elzbieta; Szczepanowski, Roman H.; Cypryk, Marek; Sobczak, Milena; Janicka, Magdalena; Kraszewska, Karina; Bartos, Paulina; Chwialkowska, Anna; Nawrot, Barbara

    2015-01-01

    2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon–anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3′-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif. PMID:25690900

  8. A new image reconstruction method for 3-D PET based upon pairs of near-missing lines of response

    NASA Astrophysics Data System (ADS)

    Kawatsu, Shoji; Ushiroya, Noboru

    2007-02-01

    We formerly introduced a new image reconstruction method for three-dimensional positron emission tomography, which is based upon pairs of near-missing lines of response. This method uses an elementary geometric property of lines of response, namely that two lines of response which originate from radioactive isotopes located within a sufficiently small voxel, will lie within a few millimeters of each other. The effectiveness of this method was verified by performing a simulation using GATE software and a digital Hoffman phantom.

  9. Configurable spatiotemporal properties in a photon-pair source based on spontaneous four-wave mixing with multiple transverse modes.

    PubMed

    Cruz-Delgado, Daniel; Monroy-Ruz, Jorge; Barragan, Angela M; Ortiz-Ricardo, Erasto; Cruz-Ramirez, Hector; Ramirez-Alarcon, Roberto; Garay-Palmett, Karina; U'Ren, Alfred B

    2014-06-15

    We present an experimental and theoretical study of photon pairs generated by spontaneous four-wave mixing (SFWM), based on birefringent phasematching, in a fiber that supports more than one transverse mode. We present SFWM spectra, obtained through single-channel and coincidence photon counting, which exhibit multiple peaks shown here to be the result of multiple SFWM processes associated with different combinations of transverse modes for the pump, signal, and idler waves.

  10. Exchange coupling between laterally adjacent nanomagnets

    NASA Astrophysics Data System (ADS)

    Dey, H.; Csaba, G.; Bernstein, G. H.; Porod, W.

    2016-09-01

    We experimentally demonstrate exchange-coupling between laterally adjacent nanomagnets. Our results show that two neighboring nanomagnets that are each antiferromagnetically exchange-coupled to a common ferromagnetic bottom layer can be brought into strong ferromagnetic interaction. Simulations show that interlayer exchange coupling effectively promotes ferromagnetic alignment between the two nanomagnets, as opposed to antiferromagnetic alignment due to dipole-coupling. In order to experimentally demonstrate the proposed scheme, we fabricated arrays of pairs of elongated, single-domain nanomagnets. Magnetic force microscopy measurements show that most of the pairs are ferromagnetically ordered. The results are in agreement with micromagnetic simulations. The presented scheme can achieve coupling strengths that are significantly stronger than dipole coupling, potentially enabling far-reaching applications in Nanomagnet Logic, spin-wave devices and three-dimensional storage and computing.

  11. ARPES measurements of the superconducting gap of Fe-based superconductors and their implications to the pairing mechanism.

    PubMed

    Richard, P; Qian, T; Ding, H

    2015-07-29

    Its direct momentum sensitivity confers to angle-resolved photoemission spectroscopy (ARPES) a unique perspective in investigating the superconducting gap of multi-band systems. In this review we discuss ARPES studies on the superconducting gap of high-temperature Fe-based superconductors. We show that while Fermi-surface-driven pairing mechanisms fail to provide a universal scheme for the Fe-based superconductors, theoretical approaches based on short-range interactions lead to a more robust and universal description of superconductivity in these materials. Our findings are also discussed in the broader context of unconventional superconductivity. PMID:26153847

  12. Translation during cold adaptation does not involve mRNA-rRNA base pairing through the downstream box.

    PubMed

    La Teana, A; Brandi, A; O'Connor, M; Freddi, S; Pon, C L

    2000-10-01

    The downstream box (DB) has been proposed to enhance translation of several mRNAs and to be a key element controlling the expression of cold-shocked mRNAs. However, the proposal that the DB exerts its effects through a base pairing interaction with the complementary anti-downstream box (antiDB) sequence (nt 1469-1483) located in the penultimate stem (helix 44) of 16S rRNA remains controversial. The existence of this interaction during initiation of protein synthesis under cold-shock conditions has been investigated in the present work using an Escherichia coli strain whose ribosomes lack the potential to base pair with mRNA because of a 12 bp inversion of the antiDB sequence in helix 44. Our results show that this strain is capable of cold acclimation, withstands cold shock, and its ribosomes translate mRNAs that contain or lack DB sequences with similar efficiency, comparable to that of the wild type. The structure of helix 44 in 30S ribosomal subunits from cells grown at 37 degrees C and from cells subjected to cold shock was also analyzed by binding a 32P-labeled oligonucleotide complementary to the antiDB region and by chemical probing with DMS and kethoxal. Both approaches clearly indicate that this region is in a double-stranded conformation and therefore not available for base pairing with mRNA.

  13. Pick a Pair. Pancake Pairs

    ERIC Educational Resources Information Center

    Miller, Pat

    2005-01-01

    Cold February weather and pancakes are a traditional pairing. Pancake Day began as a way to eat up the foods that were abstained from in Lent--traditionally meat, fat, eggs and dairy products. The best-known pancake event is The Pancake Day Race in Buckinghamshire, England, which has been run since 1445. This column describes pairs of books that…

  14. A GIS-based methodology to quantitatively define an Adjacent Protected Area in a shallow karst cavity: the case of Altamira cave.

    PubMed

    Elez, J; Cuezva, S; Fernandez-Cortes, A; Garcia-Anton, E; Benavente, D; Cañaveras, J C; Sanchez-Moral, S

    2013-03-30

    Different types of land use are usually present in the areas adjacent to many shallow karst cavities. Over time, the increasing amount of potentially harmful matter and energy, of mainly anthropic origin or influence, that reaches the interior of a shallow karst cavity can modify the hypogeal ecosystem and increase the risk of damage to the Palaeolithic rock art often preserved within the cavity. This study proposes a new Protected Area status based on the geological processes that control these matter and energy fluxes into the Altamira cave karst system. Analysis of the geological characteristics of the shallow karst system shows that direct and lateral infiltration, internal water circulation, ventilation, gas exchange and transmission of vibrations are the processes that control these matter and energy fluxes into the cave. This study applies a comprehensive methodological approach based on Geographic Information Systems (GIS) to establish the area of influence of each transfer process. The stratigraphic and structural characteristics of the interior of the cave were determined using 3D Laser Scanning topography combined with classical field work, data gathering, cartography and a porosity-permeability analysis of host rock samples. As a result, it was possible to determine the hydrogeological behavior of the cave. In addition, by mapping and modeling the surface parameters it was possible to identify the main features restricting hydrological behavior and hence direct and lateral infiltration into the cave. These surface parameters included the shape of the drainage network and a geomorphological and structural characterization via digital terrain models. Geological and geomorphological maps and models integrated into the GIS environment defined the areas involved in gas exchange and ventilation processes. Likewise, areas that could potentially transmit vibrations directly into the cave were identified. This study shows that it is possible to define a

  15. Murine neurovirulence studies with a chimeric poliovirus: in vivo generation of a mutant base-paired stable attenuated poliovirus.

    PubMed

    Lee, C; Young, C

    1998-10-01

    We investigated the neurovirulence of a chimeric poliovirus consisting of the coding region of Lansing type 2 poliovirus and the 5'NCR of type 3 poliovirus. Specifically we carried out studies on the effects of stable base pairing, between nucleotides 472 and 537, on neurovirulence. Mice were injected intracranially with the attenuated chimeric virus MAS 27 plaque 1 having the following nucleotide base pair at 472-537, G-G. Mutants recovered from the CNS of inoculated mice were divided into three groups according to the nucleotide sequence of the 5'NCR; MAS 27C type viruses having a single base change (G-C) at the position 472, MAS 27G type mutants having a single base change (G-C) at the position 537, and MAS 27U type viruses having a single base change (G-U) at the position 537. The isolate MAS 27C had back-mutated to the wild type, and 100 000 fold more virulent than attenuated MAS 27G and MAS 27U. MAS 27C type mutants were predominant, suggesting that base C at position 472 is favoured to form a stable secondary structure with guanine at position 537. Attenuated MAS 27G, however, carries guanine and cytosine at nucleotides 472 and 537 respectively, and was a stable attenuated virus following passage in four serial generations of mice. Furthermore, attenuated MAS 27G poliovirus produced viral proteins less efficiently and had slower growth rates than the revertant MAS 27C. The stable attenuated base paired MAS 27G might provide the basis for a prototype for a live attenuated stable type 3 poliovaccine.

  16. Path integral molecular dynamics method based on a pair density matrix approximation: An algorithm for distinguishable and identical particle systems

    NASA Astrophysics Data System (ADS)

    Miura, Shinichi; Okazaki, Susumu

    2001-09-01

    In this paper, the path integral molecular dynamics (PIMD) method has been extended to employ an efficient approximation of the path action referred to as the pair density matrix approximation. Configurations of the isomorphic classical systems were dynamically sampled by introducing fictitious momenta as in the PIMD based on the standard primitive approximation. The indistinguishability of the particles was handled by a pseudopotential of particle permutation that is an extension of our previous one [J. Chem. Phys. 112, 10 116 (2000)]. As a test of our methodology for Boltzmann statistics, calculations have been performed for liquid helium-4 at 4 K. We found that the PIMD with the pair density matrix approximation dramatically reduced the computational cost to obtain the structural as well as dynamical (using the centroid molecular dynamics approximation) properties at the same level of accuracy as that with the primitive approximation. With respect to the identical particles, we performed the calculation of a bosonic triatomic cluster. Unlike the primitive approximation, the pseudopotential scheme based on the pair density matrix approximation described well the bosonic correlation among the interacting atoms. Convergence with a small number of discretization of the path achieved by this approximation enables us to construct a method of avoiding the problem of the vanishing pseudopotential encountered in the calculations by the primitive approximation.

  17. A simplified concentration series to produce a pair of 2D asynchronous spectra based on the DAOSD approach

    NASA Astrophysics Data System (ADS)

    Kang, Xiaoyan; He, Anqi; Guo, Ran; Zhai, Yanjun; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

    2016-11-01

    We propose a substantially simplified approach to construct a pair of 2D asynchronous spectra based on the DAOSD approach proposed in our previous papers. By using a new concentration series, only three 1D spectra are used to generate a pair of 2D correlation spectra together with two reference spectra. By using this method, the previous problem of labor intensive traditional DAOSD approach has been successfully addressed. We apply the new approach to characterize intermolecular interaction between acetonitrile and butanone dissolved in carbon tetrachloride. The existence of intermolecular interaction between the two solutes can be confirmed by the presence of a cross peak in the resultant 2D IR spectra. In addition, the absence of cross peak around (2254, 2292) in Ψbutanone provides another experimental evidence to reveal the intrinsic relationship between the Ctbnd N stretching band and an overtone band (δCH3+νC-C).

  18. Use of pK(a) differences to enhance the formation of base triplets involving C-G and G-C base pairs.

    PubMed

    Chen, D L; McLaughlin, L W

    2000-11-01

    Two C-nucleosides are employed for the recognition of dC-dG base pairs. Both derivatives are related to dC but lack the O2-carbonyl. The absence of the carbonyl should eliminate any unfavorable steric interactions at this site. One of the derivatives contains a 2-aminopyridine heterocycle (d2APy) while the second contains a 2-aminopyrimidine heterocycle (d2APm). The former with a pK(a) of 6. 8 functions better for the recognition of dG-dC base pairs than it does in the binding to dC-dG base pairs. The d2APm derivative with a pK(a) of 3.3 functions better to form base triplets with dC-dG base pairs than with dG-dC targets. Triplex T(m)'s in both cases are compared with the sequence containing the native dC residue. The dC analogues appear to make two hydrogen bonds to a target dG base residue, one of which requires protonation of the ring nitrogen. Recognition of a target dC residue appears to require the formation of a single hydrogen bond to the C-nucleoside and having that nitrogen largely in the unprotonated state facilitates its formation.

  19. High-efficiency all-polymer solar cells based on a pair of crystalline low-bandgap polymers.

    PubMed

    Mu, Cheng; Liu, Peng; Ma, Wei; Jiang, Kui; Zhao, Jingbo; Zhang, Kai; Chen, Zhihua; Wei, Zhanhua; Yi, Ya; Wang, Jiannong; Yang, Shihe; Huang, Fei; Facchetti, Antonio; Ade, Harald; Yan, He

    2014-11-12

    All-polymer solar cells based on a pair of crystalline low-bandgap polymers (NT and N2200) are demonstrated to achieve a high short-circuit current density of 11.5 mA cm-2 and a power conversion efficiency of up to 5.0% under the standard AM1.5G spectrum with one sun intensity. The high performance of these NT:N2200-based cells can be attributed to the low optical bandgaps of the polymers and the reasonably high and balanced electron and hole mobilities of the NT:N2200 blends due to the crystalline nature of the two polymers.

  20. Alpha-beta monitoring system based on pair of simultaneous Multi-Wire Proportional Counters

    NASA Astrophysics Data System (ADS)

    Wengrowicz, U.; Amidan, D.; Orion, I.

    2016-08-01

    A new approach for a simultaneous alpha-beta Multi-wire Proportional Counter (MWPC) is presented. The popular approach for alpha-beta monitoring systems consists of a large area MWPC using noble gas flow such as Argon Methane. This method of measurement is effective but requires large-scale and expensive maintenance due to the needs of gas flow control and periodic replacements. In this work, a pair of simultaneous MWPCs for alpha-beta measuring is presented. The developed detector consists of a sealed gas MWPC sensor for beta particles, behind a free air alpha sensor. This approach allows effective simultaneous detection and discrimination of both alpha and beta radiation without the maintenance cost noble gas flow required for unsealed detectors.

  1. The ALHAMBRA survey: An empirical estimation of the cosmic variance for merger fraction studies based on close pairs

    NASA Astrophysics Data System (ADS)

    López-Sanjuan, C.; Cenarro, A. J.; Hernández-Monteagudo, C.; Varela, J.; Molino, A.; Arnalte-Mur, P.; Ascaso, B.; Castander, F. J.; Fernández-Soto, A.; Huertas-Company, M.; Márquez, I.; Martínez, V. J.; Masegosa, J.; Moles, M.; Pović, M.; Aguerri, J. A. L.; Alfaro, E.; Aparicio-Villegas, T.; Benítez, N.; Broadhurst, T.; Cabrera-Caño, J.; Cepa, J.; Cerviño, M.; Cristóbal-Hornillos, D.; Del Olmo, A.; González Delgado, R. M.; Husillos, C.; Infante, L.; Perea, J.; Prada, F.; Quintana, J. M.

    2014-04-01

    Aims: Our goal is to estimate empirically the cosmic variance that affects merger fraction studies based on close pairs for the first time. Methods: We compute the merger fraction from photometric redshift close pairs with 10 h-1 kpc ≤ rp ≤ 50 h-1 kpc and Δv ≤ 500 km s-1 and measure it in the 48 sub-fields of the ALHAMBRA survey. We study the distribution of the measured merger fractions that follow a log-normal function and estimate the cosmic variance σv as the intrinsic dispersion of the observed distribution. We develop a maximum likelihood estimator to measure a reliable σv and avoid the dispersion due to the observational errors (including the Poisson shot noise term). Results: The cosmic variance σv of the merger fraction depends mainly on (i) the number density of the populations under study for both the principal (n1) and the companion (n2) galaxy in the close pair and (ii) the probed cosmic volume Vc. We do not find a significant dependence on either the search radius used to define close companions, the redshift, or the physical selection (luminosity or stellar mass) of the samples. Conclusions: We have estimated the cosmic variance that affects the measurement of the merger fraction by close pairs from observations. We provide a parametrisation of the cosmic variance with n1, n2, and Vc, σv ∝ n1-0.54Vc-0.48 (n_2/n_1)-0.37 . Thanks to this prescription, future merger fraction studies based on close pairs could properly account for the cosmic variance on their results. Based on observations collected at the German-Spanish Astronomical Center, Calar Alto, jointly operated by the Max-Planck-Institut für Astronomie (MPIA) at Heidelberg and the Instituto de Astrofísica de Andalucía (IAA-CSIC).Appendix is available in electronic form at http://www.aanda.org

  2. A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties.

    PubMed

    Tiller, Thomas; Schuster, Ingrid; Deppe, Dorothée; Siegers, Katja; Strohner, Ralf; Herrmann, Tanja; Berenguer, Marion; Poujol, Dominique; Stehle, Jennifer; Stark, Yvonne; Heßling, Martin; Daubert, Daniela; Felderer, Karin; Kaden, Stefan; Kölln, Johanna; Enzelberger, Markus; Urlinger, Stefanie

    2013-01-01

    This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds.

  3. A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties

    PubMed Central

    Tiller, Thomas; Schuster, Ingrid; Deppe, Dorothée; Siegers, Katja; Strohner, Ralf; Herrmann, Tanja; Berenguer, Marion; Poujol, Dominique; Stehle, Jennifer; Stark, Yvonne; Heßling, Martin; Daubert, Daniela; Felderer, Karin; Kaden, Stefan; Kölln, Johanna; Enzelberger, Markus; Urlinger, Stefanie

    2013-01-01

    This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds. PMID:23571156

  4. Attacking mechanism of hydroxyl radical to DNA base-pair: density functional study in vacuum and in water.

    PubMed

    Shimizu, Eisuke; Tokuyama, Yuki; Okutsu, Naoko; Nomura, Kazuya; Danilov, Victor I; Kurita, Noriyuki

    2015-01-01

    Recently, the influence of radiation on human body has been recognized as a serious problem. In particular, highly reactive hydroxyl radicals *OH produced by the radiation react with DNA, resulting in a great damage on its structure and electronic properties. It is thus important to investigate the reaction mechanism of *OH to DNA for elucidating the initial damage in DNA induced by the radiation. In the present study, we search for transition states (TS) of the reaction between G-C/A-T base-pair and [Formula: see text] in vacuum and in water, by the density functional theory (DFT) calculations. At first, we obtain the stable structures for the dehydrogenated G-C and A-T, in which the hydrogen atom of NH2 group of G or A base is abstracted by [Formula: see text]. From the structures of the dehydrogenated as well as the natural base-pairs, the TS between these structures is searched for and the activation free energy (AFE) is estimated for the reaction. In vacuum, AFEs for the G-C and A-T are almost the same each other, while the stabilization energy by the reaction for G-C is about 4.9 kcal/mol larger than that for A-T, indicating that the population of the dehydrogenated G-C is remarkably larger than that of the dehydrogenated A-T in vacuum. On the other hand, in water approximated by the continuum solvation model, the AFE for A-T is 2.6 kcal/mol smaller than that for G-C, indicating that the reaction dehydrogenated by [Formula: see text] occurs more frequently for the solvated A-T base-pair than G-C.

  5. A new three-way supramolecular switch based on redox-controlled interconversion of hetero- and homo-guest-pair inclusion inside a host molecule.

    PubMed

    Hwang, Ilha; Ziganshina, Albina Y; Ko, Young Ho; Yun, Gyeongwon; Kim, Kimoon

    2009-01-28

    A novel three-way supramolecular switch based on the interconversion of hetero-guest-pair (D-A) and homo-guest-pair (D(2) or A(2)) inclusion inside cucurbit[8]uril is reported, which can be selectively controlled by chemical or electrochemical stimuli.

  6. Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair

    PubMed Central

    Cerón-Carrasco, José P.; Requena, Alberto; Zúñiga, José; Jacquemin, Denis

    2015-01-01

    We investigate the attack of the nitrogen dioxide radical (NO•2) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO•2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO•2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis. PMID:25798437

  7. Reversible phospholipid nanogels for deoxyribonucleic acid fragment size determinations up to 1500 base pairs and integrated sample stacking.

    PubMed

    Durney, Brandon C; Bachert, Beth A; Sloane, Hillary S; Lukomski, Slawomir; Landers, James P; Holland, Lisa A

    2015-06-23

    Phospholipid additives are a cost-effective medium to separate deoxyribonucleic acid (DNA) fragments and possess a thermally-responsive viscosity. This provides a mechanism to easily create and replace a highly viscous nanogel in a narrow bore capillary with only a 10°C change in temperature. Preparations composed of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) self-assemble, forming structures such as nanodisks and wormlike micelles. Factors that influence the morphology of a particular DMPC-DHPC preparation include the concentration of lipid in solution, the temperature, and the ratio of DMPC and DHPC. It has previously been established that an aqueous solution containing 10% phospholipid with a ratio of [DMPC]/[DHPC]=2.5 separates DNA fragments with nearly single base resolution for DNA fragments up to 500 base pairs in length, but beyond this size the resolution decreases dramatically. A new DMPC-DHPC medium is developed to effectively separate and size DNA fragments up to 1500 base pairs by decreasing the total lipid concentration to 2.5%. A 2.5% phospholipid nanogel generates a resolution of 1% of the DNA fragment size up to 1500 base pairs. This increase in the upper size limit is accomplished using commercially available phospholipids at an even lower material cost than is achieved with the 10% preparation. The separation additive is used to evaluate size markers ranging between 200 and 1500 base pairs in order to distinguish invasive strains of Streptococcus pyogenes and Aspergillus species by harnessing differences in gene sequences of collagen-like proteins in these organisms. For the first time, a reversible stacking gel is integrated in a capillary sieving separation by utilizing the thermally-responsive viscosity of these self-assembled phospholipid preparations. A discontinuous matrix is created that is composed of a cartridge of highly viscous phospholipid assimilated into a separation matrix

  8. Cryptanalysis and Improvement on "Robust EPR-Pairs-Based Quantum Secure Communication with Authentication Resisting Collective Noise"

    NASA Astrophysics Data System (ADS)

    Yue, Qiu-Ling; Yu, Chao-Hua; Liu, Bin; Wang, Qing-Le

    2016-05-01

    Recently, Chang et al. [Sci Chin-Phys Mech Astron. 57(10), 1907-1912, 2014] proposed two robust quantum secure communication protocols with authentication based on Einstein-Podolsky-Rosen (EPR) pairs, which can resist collective noise. In this paper, we analyze the security of their protocols, and show that there is a kind of security flaw in their protocols. By a kind of impersonation attack, the eavesdropper can obtain half of the message on average. Furthermore, an improved method of their protocols is proposed to close the security loophole.

  9. Cryptanalysis and Improvement on "Robust EPR-Pairs-Based Quantum Secure Communication with Authentication Resisting Collective Noise"

    NASA Astrophysics Data System (ADS)

    Yue, Qiu-Ling; Yu, Chao-Hua; Liu, Bin; Wang, Qing-Le

    2016-10-01

    Recently, Chang et al. [Sci Chin-Phys Mech Astron. 57(10), 1907-1912, 2014] proposed two robust quantum secure communication protocols with authentication based on Einstein-Podolsky-Rosen (EPR) pairs, which can resist collective noise. In this paper, we analyze the security of their protocols, and show that there is a kind of security flaw in their protocols. By a kind of impersonation attack, the eavesdropper can obtain half of the message on average. Furthermore, an improved method of their protocols is proposed to close the security loophole.

  10. Ion pair recognition receptor based on an unsymmetrically 1,1'-disubstituted ferrocene-triazole derivative.

    PubMed

    Otón, Francisco; González, María del Carmen; Espinosa, Arturo; Ramírez de Arellano, Carmen; Tárraga, Alberto; Molina, Pedro

    2012-11-16

    The ferrocene-triazole derivative 4, available from 1,1'-bis(diazido)ferrocene by sequential functionalization through click-type chemistry and the Staudinger reaction, is elaborated as a lab-on-a-molecule for the selective sensing of HP(2)O(7)(3-) and Hg(2+). Receptor 4 behaves as a ratiometric fluorescent probe for HP(2)O(7)(3-) with a good selectivity over other anions, whereas in the presence of Hg(2+) it modifies the fluorescent emission of the pyrene unit, acting as a selective on-off fluorescent sensor for Hg(2+) with a low detection limit. The most salient feature of compound 4 is its behavior as an excellent electrooptical ion pair recognition receptor able to simultaneously recognize Pb(2+) cations in the presence of HP(2)O(7)(3-) anion through multichannel perturbations of the redox potential of the ferrocene unit, the emission spectrum, and a noticeable color change from yellow to green.

  11. Robustness of quantum critical pairing against disorder in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Kang, Jian; Fernandes, Rafael

    Several experiments in iron pnictides and cuprates reveal a superconducting (SC) state remarkably robust against non-magnetic disorder -- at least when compared to the simple extension of the Abrikosov-Gor'kov formalism to dirty unconventional superconductors. Motivated by the fact that most of these SC states appear in proximity to a magnetic instability, here we study the impact of non-magnetic disorder on the SC state promoted by quantum critical magnetic fluctuations. We go beyond the weak coupling approach by applying a variational formalism of the Eliashberg equations of the spin-fermion model, taking into account the effects of disorder on both fermionic and bosonic degrees of freedom. We find that the reduced fermionic coherent spectral weight near the magnetic quantum critical point strongly decreases the suppression rate of Tc by weak disorder, as compared to the Abrikosov-Gor'kov universal value. Furthermore, because the bosons promoting the Cooper pairs emerge as collective modes of the fermions, they are also impacted by disorder, giving rise to an additional reduction of the suppression rate of Tc by weak disorder. Our results qualitatively agree with experiments, shedding new light on why unconventional superconductors are robust against disorder. This work is supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, under Award Number DE-SC0012336.

  12. Variable electron transfer pathways in an amphibian cryptochrome: tryptophan versus tyrosine-based radical pairs.

    PubMed

    Biskup, Till; Paulus, Bernd; Okafuji, Asako; Hitomi, Kenichi; Getzoff, Elizabeth D; Weber, Stefan; Schleicher, Erik

    2013-03-29

    Electron transfer reactions play vital roles in many biological processes. Very often the transfer of charge(s) proceeds stepwise over large distances involving several amino acid residues. By using time-resolved electron paramagnetic resonance and optical spectroscopy, we have studied the mechanism of light-induced reduction of the FAD cofactor of cryptochrome/photolyase family proteins. In this study, we demonstrate that electron abstraction from a nearby amino acid by the excited FAD triggers further electron transfer steps even if the conserved chain of three tryptophans, known to be an effective electron transfer pathway in these proteins, is blocked. Furthermore, we were able to characterize this secondary electron transfer pathway and identify the amino acid partner of the resulting flavin-amino acid radical pair as a tyrosine located at the protein surface. This alternative electron transfer pathway could explain why interrupting the conserved tryptophan triad does not necessarily alter photoreactions of cryptochromes in vivo. Taken together, our results demonstrate that light-induced electron transfer is a robust property of cryptochromes and more intricate than commonly anticipated.

  13. Robust silver-mediated imidazolo-dC base pairs in metal DNA: dinuclear silver bridges with exceptional stability in double helices with parallel and antiparallel strand orientation.

    PubMed

    Jana, Sunit Kumar; Guo, Xiurong; Mei, Hui; Seela, Frank

    2015-12-18

    A new unprecedented metal-mediated base pair was designed that stabilizes reverse Watson-Crick DNA (parallel strand orientation, ps) as well as canonical Watson-Crick DNA (antiparallel strand orientation, aps). This base pair contains two imidazolo-dC units decorated with furan residues. Tm measurements and spectroscopic studies reveal that each silver-mediated furano-imidazolo-dC forms exceptionally stable duplexes with ps and aps chain orientation. This stability increase by a silver-mediated base pair is the highest reported so far for ps and aps DNA helices. PMID:26463426

  14. Salt dependent premelting base pair opening probabilities of B and Z DNA Poly [d(G-C)] and significance for the B-Z transition

    PubMed Central

    Chen, Y. Z.; Prohofsky, E. W.

    1993-01-01

    We calculate room temperature thermal fluctuational base pair opening probabilities of B and Z DNA Poly[d(G-C)] at various salt concentrations and discuss the significance of thermal fluctuation in facilitating base pair disruption during B to Z transition. Our calculated base pair opening probability of the B DNA at lower salt concentrations and the probability of the Z DNA at high salt concentrations are in agreement with observations. The salt dependence of the probabilities indicates a B to Z transition at a salt concentration close to the observed concentration. PMID:19431893

  15. Analysis of difference spectra of protonated DNA: determination of degree of protonation of nitrogen bases and the fractions of disordered nucleotide pairs.

    PubMed Central

    Smol'janinova, T I; Zhidkov, V A; Sokolov, G V

    1982-01-01

    The titration curves of nitrogen bases and fractions of disordered nucleotide pairs are obtained during DNA protonation. It is shown that purine bases are the first sites of the DNA double helix protonation. The cytosine protonation is due to proton-induced conformational transition within GC pairs with the sequence proton transfer from (N-7) of guanine to (N-3) of cytosine. Within DNA with unwound regions the bases are protonated in the following order: cytosine, adenine, guanine. It is shown that GC pairs are the primary centres in which the unwinding of protonated DNAs occurs. PMID:7079177

  16. Base pairing within the psi32,psi39-modified anticodon arm of Escherichia coli tRNA(Phe).

    PubMed

    Tworowska, Izabela; Nikonowicz, Edward P

    2006-12-13

    The base-base hydrogen bond interactions of the psi32,psi39-modified anticodon arm of Escherichia coli tRNAPhe have been investigated using heteronuclear NMR spectroscopy. psi32 and psi39 were enzymatically introduced into a [13C,15N]-isotopically enriched RNA sequence corresponding to the tRNAPhe anticodon arm. Both the psi32-A38 and A31-psi39 nucleotide pairs form Watson-Crick base pairing schemes and the anticodon nucleotides adopt a triloop conformation. Similar effects were observed previously with D2-isopentenyl modification of the A37 N6 that also is native to the tRNAPhe anticodon arm. These results demonstrate that the individual modifications are not sufficient to produce the 32-38 bifurcated hydrogen bond or the U-turn motifs that are observed in crystal structures of tRNAs and tRNA-protein complexes. Thus the formation of these conserved structural features in solution likely require the synergistic interaction of multiple modifications.

  17. Experimental demonstration of wavelength domain rogue-free ONU based on wavelength-pairing for TDM/WDM optical access networks.

    PubMed

    Lee, Jie Hyun; Park, Heuk; Kang, Sae-Kyoung; Lee, Joon Ki; Chung, Hwan Seok

    2015-11-30

    In this study, we propose and experimentally demonstrate a wavelength domain rogue-free ONU based on wavelength-pairing of downstream and upstream signals for time/wavelength division-multiplexed optical access networks. The wavelength-pairing tunable filter is aligned to the upstream wavelength channel by aligning it to one of the downstream wavelength channels. Wavelength-pairing is implemented with a compact and cyclic Si-AWG integrated with a Ge-PD. The pairing filter covered four 100 GHz-spaced wavelength channels. The feasibility of the wavelength domain rogue-free operation is investigated by emulating malfunction of the misaligned laser. The wavelength-pairing tunable filter based on the Si-AWG blocks the upstream signal in the non-assigned wavelength channel before data collision with other ONUs.

  18. Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase

    SciTech Connect

    Reha-Krantz, Linda J.; Hariharan, Chithra; Subuddhi, Usharani; Xia, Shuangluo; Zhao, Chao; Beckman, Jeff; Christian, Thomas; Konigsberg, William

    2011-11-21

    The adenine base analogue 2-aminopurine (2AP) is a potent base substitution mutagen in prokaryotes because of its enhanceed ability to form a mutagenic base pair with an incoming dCTP. Despite more than 50 years of research, the structure of the 2AP-C base pair remains unclear. We report the structure of the 2AP-dCTP base pair formed within the polymerase active site of the RB69 Y567A-DNA polymerase. A modified wobble 2AP-C base pair was detected with one H-bond between N1 of 2AP and a proton from the C4 amino group of cytosine and an apparent bifurcated H-bond between a proton on the 2-amino group of 2-aminopurine and the ring N3 and O2 atoms of cytosine. Interestingly, a primer-terminal region rich in AT base pairs, compared to GC base pairs, facilitated dCTP binding opposite template 2AP. We propose that the increased flexibility of the nucleotide binding pocket formed in the Y567A-DNA polymerase and increased 'breathing' at the primer-terminal junction of A+T-rich DNA facilitate dCTP binding opposite template 2AP. Thus, interactions between DNA polymerase residues with a dynamic primer-terminal junction play a role in determining base selectivity within the polymerase active site of RB69 DNA polymerase.

  19. Graphene oxide and metal-mediated base pairs based "molecular beacon" integrating with exonuclease I for fluorescence turn-on detection of biothiols.

    PubMed

    Xing, Xiaojing; Zhou, Ying; Liu, Xueguo; Pang, Daiwen; Tang, Hongwu

    2014-08-27

    A novel fluorescence turn-on strategy, based on the resistance of metal-mediated molecular-beacons (MBs) toward nuclease digestion and the remarkable difference in the affinity of graphene oxide (GO) with MBs and the mononucleotides, is designed for the biothiols assay. Specifically, the metal-mediated base pairs facilitate the dye labeled MBs to fold into a hairpin structure preventing the digestion by exonuclease I, and thus allow the fluorescence quenching. The competition binding by biothiols removes metal ions from the base pairs, causing the nuclease reaction, and less decrease in the fluorescence is obtained after incubating with GO due to the weak affinity of the product-mononucleotides to GO. Hg(2+)-mediated MBs were firstly designed for the biothiols detection, and glutathione (GSH) was applied as the model target. Under the optimal conditions, the approach exhibits high sensitivity to GSH with a detection limit of 1.53 nM. Ag(+)-mediated MBs based sensor was also constructed to demonstrate its versatility, and cysteine was studied as the model target. The satisfactory results in the determination of biothiols in serum demonstrate that the method possesses great potential for detecting thiols in biological fluids. This new approach is expected to promote the exploitation of metal-mediated base pairs-based biosensors in biochemical and biomedical studies.

  20. Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson-Crick base pairing.

    PubMed

    Berger, Or; Adler-Abramovich, Lihi; Levy-Sakin, Michal; Grunwald, Assaf; Liebes-Peer, Yael; Bachar, Mor; Buzhansky, Ludmila; Mossou, Estelle; Forsyth, V Trevor; Schwartz, Tal; Ebenstein, Yuval; Frolow, Felix; Shimon, Linda J W; Patolsky, Fernando; Gazit, Ehud

    2015-04-01

    The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise base pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs-CG, GC and GG-could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick base pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.

  1. Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson-Crick base pairing

    NASA Astrophysics Data System (ADS)

    Berger, Or; Adler-Abramovich, Lihi; Levy-Sakin, Michal; Grunwald, Assaf; Liebes-Peer, Yael; Bachar, Mor; Buzhansky, Ludmila; Mossou, Estelle; Forsyth, V. Trevor; Schwartz, Tal; Ebenstein, Yuval; Frolow, Felix; Shimon, Linda J. W.; Patolsky, Fernando; Gazit, Ehud

    2015-05-01

    The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise base pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs—CG, GC and GG—could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick base pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.

  2. Reaction of systemic lupus erythematosus antinative DNA antibodies with native DNA fragments from 20 to 1,200 base pairs.

    PubMed Central

    Papalian, M; Lafer, E; Wong, R; Stollar, B D

    1980-01-01

    Double-stranded DNA fragments of varying sizes were isolated and tested for binding to systemic lupus erythematosus (SLE) antinative DNA antibodies. Fragments of 20-25, 40-50, 90-110, and 160-180 base pairs (bp), along with intermediate-size pieces were isolated by preparative gel electrophoresis of a limited micrococcal nuclease digest of calf thymus DNA. Larger helical polynucleotides of 160-200, 380, 600-1,000, and 1,200 bp were isolated by preparative gel electrophoresis of DNA from chicken erythrocyte nucleosomes and oligonucleosomes. The fragments behaved as base-paired structures as tested by thermal denaturation, resistance to S1 nuclease, and serological assays with antibodies to native or denatured DNA. At a concentration of 0.27 muM, fragments of 20-25 bp were able to react with two SLE sera in competition with native DNA. With these and two other sera, DNA of 40-50 bp was a much more effective competitor. One serum required DNA greater than 180 bp for competition in the concentration range tested. Denatured fragments were much less effective than native fragments. The results emphasize the heterogeneity of SLE antinative DNA antibodies, confirm that secondary structure of the antigen is important for specific binding to these antibodies, and support the suggestion that bivalent binding to one molecule may be important for high functional affinity. Images PMID:6153184

  3. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition

    PubMed Central

    Harika, Narinder K.; Paul, Ananya; Stroeva, Ekaterina; Chai, Yun; Boykin, David W.; Germann, Markus W.; Wilson, W. David

    2016-01-01

    Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents. PMID:27131382

  4. Computational DNA hole spectroscopy: A new tool to predict mutation hotspots, critical base pairs, and disease ‘driver’ mutations

    PubMed Central

    Suárez, Martha Y.; Villagrán; Miller, John H.

    2015-01-01

    We report on a new technique, computational DNA hole spectroscopy, which creates spectra of electron hole probabilities vs. nucleotide position. A hole is a site of positive charge created when an electron is removed. Peaks in the hole spectrum depict sites where holes tend to localize and potentially trigger a base pair mismatch during replication. Our studies of mitochondrial DNA reveal a correlation between L-strand hole spectrum peaks and spikes in the human mutation spectrum. Importantly, we also find that hole peak positions that do not coincide with large variant frequencies often coincide with disease-implicated mutations and/or (for coding DNA) encoded conserved amino acids. This enables combining hole spectra with variant data to identify critical base pairs and potential disease ‘driver’ mutations. Such integration of DNA hole and variance spectra could ultimately prove invaluable for pinpointing critical regions of the vast non-protein-coding genome. An observed asymmetry in correlations, between the spectrum of human mtDNA variations and the L- and H-strand hole spectra, is attributed to asymmetric DNA replication processes that occur for the leading and lagging strands. PMID:26310834

  5. Young Foreign Language Learners' Interactions during Task-Based Paired Assessments

    ERIC Educational Resources Information Center

    Butler, Yuko Goto; Zeng, Wei

    2014-01-01

    Despite the popularity of task-based language teaching (TBLT) in foreign language (FL) education at elementary school, it remains unclear how young learners' FL abilities can best be evaluated with tasks. The present study seeks to understand developmental differences in interactions among elementary-school students during task-based language…

  6. Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals.

    PubMed

    Otsuka, Jinya; Sugaya, Nobuyoshi

    2003-06-21

    The ribosomal RNAs (rRNAs) of animal mitochondria, especially those of arthropod mitochondria, have a higher content of G:U and U:G base pairs in their stem regions than the nuclear rRNAs. Thus, the theoretical formulation of base pair changes is extended to incorporate the faster base pair changes A:U<-->G:U<-->G:C and U:A<-->U:G<-->C:G into the previous formulation of the slower base pair changes between A:U, G:C, C:G and U:A. The relative base pair change probability containing the faster and slower base pair changes is theoretically derived to estimate the divergence time of rRNAs under the influence of selection for these base pairs. Using the cartilaginous fish-teleost fish divergence and the crustacean-insect divergence as calibration points, the present method successfully predicts the divergence times of the main branches of animals: Deuterostomia and Protostomia diverged 9.2 x 10(8) years ago, the divergence of Echinodermata, Hemichordata and Cephalochordata succeedingly occurred during the period from 8 x 10(8) to 6 x 10(8) years ago, while Arthropoda, Annelida and Mollusca diverged almost concomitantly about 7 x 10(8) years ago. The dating for the divergence of Platyhelminthes and Cnidaria is traced back to 1.2 x 10(9) years ago. This result is consistent with the fossil records in the Stirling Range Formation of southwestern Australia, the Ediacara and Avalon faunas and the Cambrian Burgess Shale. Thus, the present method may be useful for estimating the divergence times of animals ranging from 10(8) to 10(9) years ago, resolving the difficult problems, e.g. deviation from rate constancy and large sampling variances, in the usual methods of treating apparent change rates between individual bases and/or base pairs. PMID:12781743

  7. Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals.

    PubMed

    Otsuka, Jinya; Sugaya, Nobuyoshi

    2003-06-21

    The ribosomal RNAs (rRNAs) of animal mitochondria, especially those of arthropod mitochondria, have a higher content of G:U and U:G base pairs in their stem regions than the nuclear rRNAs. Thus, the theoretical formulation of base pair changes is extended to incorporate the faster base pair changes A:U<-->G:U<-->G:C and U:A<-->U:G<-->C:G into the previous formulation of the slower base pair changes between A:U, G:C, C:G and U:A. The relative base pair change probability containing the faster and slower base pair changes is theoretically derived to estimate the divergence time of rRNAs under the influence of selection for these base pairs. Using the cartilaginous fish-teleost fish divergence and the crustacean-insect divergence as calibration points, the present method successfully predicts the divergence times of the main branches of animals: Deuterostomia and Protostomia diverged 9.2 x 10(8) years ago, the divergence of Echinodermata, Hemichordata and Cephalochordata succeedingly occurred during the period from 8 x 10(8) to 6 x 10(8) years ago, while Arthropoda, Annelida and Mollusca diverged almost concomitantly about 7 x 10(8) years ago. The dating for the divergence of Platyhelminthes and Cnidaria is traced back to 1.2 x 10(9) years ago. This result is consistent with the fossil records in the Stirling Range Formation of southwestern Australia, the Ediacara and Avalon faunas and the Cambrian Burgess Shale. Thus, the present method may be useful for estimating the divergence times of animals ranging from 10(8) to 10(9) years ago, resolving the difficult problems, e.g. deviation from rate constancy and large sampling variances, in the usual methods of treating apparent change rates between individual bases and/or base pairs.

  8. Activation Energies for Dissociation of Double Strand Oligonucleotide Anions: Evidence for Watson–Crick Base Pairing in Vacuo

    PubMed Central

    Schnier, Paul D.; Klassen, John S.; Strittmatter, Eric F.; Williams*, Evan R.

    2005-01-01

    The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)23−, (CCGG)23−, (AATTAAT)23−, (CCGGCCG)23−, A7·T73−, A7·A73−, T7·T73−, and A7·C73− were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 1013 to 1019 s−1. Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a – base) and w ions. Four pieces of evidence are presented which indicate that Watson–Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A7·T73−, to the single strands is significantly higher than that for the related noncomplementary A7·A73− and T7·T73− dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A7·A73− and A7·C73− but not for A7·T73− consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (−ΔHd) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A7·T73− duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent. PMID:16498487

  9. Longitudinal displacements of base pairs in DNA and effects on the dynamics of nonlinear excitations.

    PubMed

    Di Garbo, Angelo

    2013-09-01

    A model of the DNA is proposed and studied analytically and numerically. The model is an extension of a well known model and describes the double helix as two chains of pendula (each pendulum representing a base). Each base (or pendulum) can rotate and translate along the helix axis. In the continuum limit the system is described by the perturbed Sine-Gordon equation describing the twist of the bases and by a nonlinear partial differential equation (PDE) describing the longitudinal displacements of the bases. This coupled system of PDEs was studied analytically using different approaches and the corresponding results were tested through numerical simulations. It was found that if the coupling parameters satisfy a well defined relationship, then there exist bounded travelling wave solutions.

  10. Longitudinal displacements of base pairs in DNA and effects on the dynamics of nonlinear excitations.

    PubMed

    Di Garbo, Angelo

    2013-09-01

    A model of the DNA is proposed and studied analytically and numerically. The model is an extension of a well known model and describes the double helix as two chains of pendula (each pendulum representing a base). Each base (or pendulum) can rotate and translate along the helix axis. In the continuum limit the system is described by the perturbed Sine-Gordon equation describing the twist of the bases and by a nonlinear partial differential equation (PDE) describing the longitudinal displacements of the bases. This coupled system of PDEs was studied analytically using different approaches and the corresponding results were tested through numerical simulations. It was found that if the coupling parameters satisfy a well defined relationship, then there exist bounded travelling wave solutions. PMID:23567838

  11. Nonmagnetic impurity resonances as a signature of sign-reversal pairing in FeAs-based superconductors.

    PubMed

    Zhang, Degang

    2009-10-30

    The energy band structure of FeAs-based superconductors is fitted by a tight-binding model with two Fe ions per unit cell and two degenerate orbitals per Fe ion. Based on this, superconductivity with extended s-wave pairing symmetry of the form cosk(x)+cosk(y) is examined. The local density of states near an impurity is also investigated by using the T-matrix approach. For the nonmagnetic scattering potential, we found that there exist two major resonances inside the gap. The height of the resonance peaks depends on the strength of the impurity potential. These in-gap resonances are originated in the Andreev's bound states due to the quasiparticle scattering between the hole Fermi surfaces around Gamma point with positive order parameter and the electron Fermi surfaces around M point with negative order parameter.

  12. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components.

    PubMed

    Gerling, Thomas; Wagenbauer, Klaus F; Neuner, Andrea M; Dietz, Hendrik

    2015-03-27

    We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components' interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions. PMID:25814577

  13. Novel coronene-naphthalene dimide-based donor-acceptor pair for tunable charge-transfer nanostructures.

    PubMed

    Kumar, Mohit; George, Subi J

    2014-09-01

    Charge-transfer (CT) assemblies of aromatic donor (D) and acceptor (A) molecules have recently gained attention as a promising material for organic electronics and ferroelectrics. Two major factors which govern their functions are the strength of CT interaction and their supramolecular nanostructuring. Here we present coronene-naphthalenediimide (NDI)-based novel D-A pairs that form alternately stacked CT assemblies. Through systematic substitution of the NDI derivatives and studying their CT interactions with coronene, a clear understanding of the secondary forces responsible for controlling their association is gained. Finally, the use of CT-based supramolecular amphiphiles for their nanostructural engineering into ordered one-dimensional (1-D) assemblies is demonstrated. PMID:25045008

  14. The role of specialized transcription factories in chromosome pairing.

    PubMed

    Xu, Meng; Cook, Peter R

    2008-11-01

    Homologous chromosomes can pair in somatic and germ line cells, and many mechanisms have been proposed to explain how they do so. One popular class of models involves base-pairing between DNA strands catalyzed by recombination proteins, but pairing still occurs in mutants lacking the relevant functional proteins. We discuss an alternative based on two observations: transcription occurs in factories that specialize in transcribing specific gene sub-sets, and chromosomes only pair when transcribed. Each chromosome in the haploid set has a unique array of transcription units strung along its length; we suggest each is organized into clouds of loops tethered to specialized factories. Only homologs share similar strings of clouds and factories. Pairing begins when a promoter on one chromosome initiates in the homologous and specialized factory organized mainly by its homologous partner. This transiently ties the two homologs together, to increase the chances that adjacent promoters initiate in their homologous factories and that the two homologs will be zipped together. Then, interactions between promoters and RNA polymerases in the factories mediate pairing.

  15. A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

    USGS Publications Warehouse

    Lemons, Patrick R.; Marshall, T.C.; McCloskey, Sarah E.; Sethi, S.A.; Schmutz, Joel A.; Sedinger, James S.

    2015-01-01

    Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artifacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.

  16. Demonstration of polarization sensitivity of emulsion-based pair conversion telescope for cosmic gamma-ray polarimetry

    NASA Astrophysics Data System (ADS)

    Ozaki, Keita; Takahashi, Satoru; Aoki, Shigeki; Kamada, Keiki; Kaneyama, Taichi; Nakagawa, Ryo; Rokujo, Hiroki

    2016-10-01

    Linear polarization of high-energy gamma-rays (10MeV-100 GeV) can be detected by measuring the azimuthal angle of electron-positron pairs and observing the modulation of the azimuthal distribution. To demonstrate the gamma-ray polarization sensitivity of emulsion, we conducted a test using a polarized gamma-ray beam (0.8-2.4 GeV) at SPring-8/LEPS. Emulsion tracks were reconstructed using scanning data, and gamma-ray events were selected automatically. Using an optical microscope, out of the 2381 gamma-ray conversions that were observed, 1372 remained after event selection, on the azimuthal angle distribution of which we measured the modulation. From the distribution of the azimuthal angles of the selected events, a modulation factor of 0.21+0.11-0.09 was measured, from which the detection of a non-zero modulation was established with a significance of 3.06σ. This attractive polarimeter will be applied to the GRAINE project, a balloon-borne experiment that observes 10-100 GeV cosmic gamma-rays with an emulsion-based pair conversion telescope.

  17. Neuronal synapse as a memristor: modeling pair- and triplet-based STDP rule.

    PubMed

    Cai, Weiran; Ellinger, Frank; Tetzlaff, Ronald

    2015-02-01

    We propose a new memristive model for the neuronal synapse based on the spike-timing-dependent plasticity (STDP) protocol, considering both long-term and short-term plasticity in the synapse. Higher-order behavior is modeled by a memristor with adaptive thresholds, which realizes the well-established suppression principle of Froemke. We assume a mechanism of variable thresholds adapting to synaptic potentiation (LTP) and depression (LTD), which reproduces the refractory time in the weight modification. The corresponding dynamical process is governed by a set of ordinary differential equations. Interestingly, the Froemke's model and our memristive model, based on two completely different mechanisms, are found to be quantitatively equivalent for the 'pre-post-pre' case and 'post-pre-post' case. A relation of the adaptive thresholds to short-term plasticity is addressed.

  18. Electron pairing without superconductivity.

    PubMed

    Cheng, Guanglei; Tomczyk, Michelle; Lu, Shicheng; Veazey, Joshua P; Huang, Mengchen; Irvin, Patrick; Ryu, Sangwoo; Lee, Hyungwoo; Eom, Chang-Beom; Hellberg, C Stephen; Levy, Jeremy

    2015-05-14

    Strontium titanate (SrTiO3) is the first and best known superconducting semiconductor. It exhibits an extremely low carrier density threshold for superconductivity, and possesses a phase diagram similar to that of high-temperature superconductors--two factors that suggest an unconventional pairing mechanism. Despite sustained interest for 50 years, direct experimental insight into the nature of electron pairing in SrTiO3 has remained elusive. Here we perform transport experiments with nanowire-based single-electron transistors at the interface between SrTiO3 and a thin layer of lanthanum aluminate, LaAlO3. Electrostatic gating reveals a series of two-electron conductance resonances-paired electron states--that bifurcate above a critical pairing field Bp of about 1-4 tesla, an order of magnitude larger than the superconducting critical magnetic field. For magnetic fields below Bp, these resonances are insensitive to the applied magnetic field; for fields in excess of Bp, the resonances exhibit a linear Zeeman-like energy splitting. Electron pairing is stable at temperatures as high as 900 millikelvin, well above the superconducting transition temperature (about 300 millikelvin). These experiments demonstrate the existence of a robust electronic phase in which electrons pair without forming a superconducting state. Key experimental signatures are captured by a model involving an attractive Hubbard interaction that describes real-space electron pairing as a precursor to superconductivity. PMID:25971511

  19. Electron pairing without superconductivity

    NASA Astrophysics Data System (ADS)

    Levy, Jeremy

    Strontium titanate (SrTiO3) is the first and best known superconducting semiconductor. It exhibits an extremely low carrier density threshold for superconductivity, and possesses a phase diagram similar to that of high-temperature superconductors--two factors that suggest an unconventional pairing mechanism. Despite sustained interest for 50 years, direct experimental insight into the nature of electron pairing in SrTiO3 has remained elusive. Here we perform transport experiments with nanowire-based single-electron transistors at the interface between SrTiO3 and a thin layer of lanthanum aluminate, LaAlO3. Electrostatic gating reveals a series of two-electron conductance resonances--paired electron states--that bifurcate above a critical pairing field Bp of about 1-4 tesla, an order of magnitude larger than the superconducting critical magnetic field. For magnetic fields below Bp, these resonances are insensitive to the applied magnetic field; for fields in excess of Bp, the resonances exhibit a linear Zeeman-like energy splitting. Electron pairing is stable at temperatures as high as 900 millikelvin, well above the superconducting transition temperature (about 300 millikelvin). These experiments demonstrate the existence of a robust electronic phase in which electrons pair without forming a superconducting state. Key experimental signatures are captured by a model involving an attractive Hubbard interaction that describes real-space electron pairing as a precursor to superconductivity. Support from AFOSR, ONR, ARO, NSF, DOE and NSSEFF is gratefully acknowledged.

  20. Non-linguistic learning and aphasia: evidence from a paired associate and feedback-based task.

    PubMed

    Vallila-Rohter, Sofia; Kiran, Swathi

    2013-01-01

    Though aphasia is primarily characterized by impairments in the comprehension and/or expression of language, research has shown that patients with aphasia also show deficits in cognitive-linguistic domains such as attention, executive function, concept knowledge and memory. Research in aphasia suggests that cognitive impairments can impact the online construction of language, new verbal learning, and transactional success. In our research, we extend this hypothesis to suggest that general cognitive deficits influence progress with therapy. The aim of our study is to explore learning, a cognitive process that is integral to relearning language, yet underexplored in the field of aphasia rehabilitation. We examine non-linguistic category learning in patients with aphasia (n=19) and in healthy controls (n=12), comparing feedback and non-feedback based instruction. Participants complete two computer-based learning tasks that require them to categorize novel animals based on the percentage of features shared with one of two prototypes. As hypothesized, healthy controls showed successful category learning following both methods of instruction. In contrast, only 60% of our patient population demonstrated successful non-linguistic category learning. Patient performance was not predictable by standardized measures of cognitive ability. Results suggest that general learning is affected in aphasia and is a unique, important factor to consider in the field of aphasia rehabilitation. PMID:23127795

  1. Non-linguistic learning and aphasia: evidence from a paired associate and feedback-based task.

    PubMed

    Vallila-Rohter, Sofia; Kiran, Swathi

    2013-01-01

    Though aphasia is primarily characterized by impairments in the comprehension and/or expression of language, research has shown that patients with aphasia also show deficits in cognitive-linguistic domains such as attention, executive function, concept knowledge and memory. Research in aphasia suggests that cognitive impairments can impact the online construction of language, new verbal learning, and transactional success. In our research, we extend this hypothesis to suggest that general cognitive deficits influence progress with therapy. The aim of our study is to explore learning, a cognitive process that is integral to relearning language, yet underexplored in the field of aphasia rehabilitation. We examine non-linguistic category learning in patients with aphasia (n=19) and in healthy controls (n=12), comparing feedback and non-feedback based instruction. Participants complete two computer-based learning tasks that require them to categorize novel animals based on the percentage of features shared with one of two prototypes. As hypothesized, healthy controls showed successful category learning following both methods of instruction. In contrast, only 60% of our patient population demonstrated successful non-linguistic category learning. Patient performance was not predictable by standardized measures of cognitive ability. Results suggest that general learning is affected in aphasia and is a unique, important factor to consider in the field of aphasia rehabilitation.

  2. A Literature-Based Assessment of Concept Pairs as a Measure of Semantic Relatedness

    PubMed Central

    Workman, T. Elizabeth; Rosemblat, Graciela; Fiszman, Marcelo; Rindflesch, Thomas C.

    2013-01-01

    The semantic relatedness between two concepts, according to human perception, is domain-rooted and reflects prior knowledge. We developed a new method for semantic relatedness assessment that reflects human judgment, utilizing semantic predications extracted from PubMed citations by SemRep. We compared the new method to other approaches utilizing path-based, statistical, and context vector methods, using a gold standard for evaluation. The new method outperformed all others, except one variation of the context vector technique. These findings have implications in several natural language processing applications, such as serendipitous knowledge discovery. PMID:24551423

  3. Subtle Recognition of 14-Base Pair DNA Sequences via Threading Polyintercalation

    PubMed Central

    2012-01-01

    Small molecules that bind DNA in a sequence-specific manner could act as antibiotic, antiviral, or anticancer agents because of their potential ability to manipulate gene expression. Our laboratory has developed threading polyintercalators based on 1,4,5,8-naphthalene diimide (NDI) units connected in a head-to-tail fashion by flexible peptide linkers. Previously, a threading tetraintercalator composed of alternating minor–major–minor groove-binding modules was shown to bind specifically to a 14 bp DNA sequence with a dissociation half-life of 16 days [Holman, G. G., et al. (2011) Nat. Chem. 3, 875–881]. Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules. DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp. Relative affinities were found to correlate strongly with dissociation rates, while overall C2 symmetry in the DNA-binding molecule appeared to contribute to enhanced association rates. PMID:22554127

  4. Learning Non-Adjacent Regularities at Age 0 ; 7

    ERIC Educational Resources Information Center

    Gervain, Judit; Werker, Janet F.

    2013-01-01

    One important mechanism suggested to underlie the acquisition of grammar is rule learning. Indeed, infants aged 0 ; 7 are able to learn rules based on simple identity relations (adjacent repetitions, ABB: "wo fe fe" and non-adjacent repetitions, ABA: "wo fe wo", respectively; Marcus et al., 1999). One unexplored issue is…

  5. View of north side from exterior stairs of adjacent building, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View of north side from exterior stairs of adjacent building, bottom cut off by fringed buildings, view facing south-southwest - U.S. Naval Base, Pearl Harbor, Industrial X-Ray Building, Off Sixth Street, adjacent to and south of Facility No. 11, Pearl City, Honolulu County, HI

  6. Lethal osteogenesis imperfecta congenita and a 300 base pair gene deletion for an alpha 1(I)-like collagen.

    PubMed Central

    Pope, F M; Cheah, K S; Nicholls, A C; Price, A B; Grosveld, F G

    1984-01-01

    Broad boned lethal osteogenesis imperfecta is a severely crippling disease of unknown cause. By means of recombinant DNA technology a 300 base pair deletion in an alpha 1(I)-like collagen gene was detected in six patients and four complete parent-child groups including patients with this disease. One from each set of the patients' clinically unaffected parents also carried the deletion, implying that affected patients were genetic compounds. The study suggests that prenatal diagnosis should be possible with 100% accuracy in subjects without the deletion and with 50% accuracy in those who possess it (who would be either heterozygous--normal, or affected with the disease). Images FIG 1 FIG 2 FIG 3 FIG 4 PMID:6419953

  7. Cyanine-based probe\\tag-peptide pair fluorescence protein imaging and fluorescence protein imaging methods

    DOEpatents

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2013-01-15

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  8. Non-base pairing DNA provides a new dimension for controlling aptamer-linked nanoparticles and sensors.

    PubMed

    Liu, Juewen; Lu, Yi

    2007-07-11

    DNA aptamers have been recently applied as simple and fast colorimetric sensors for a wide range of molecules. A unique feature of these systems is the presence of non-base pairing oligonucleotides in both DNA aptamers and spacers on DNA-functionalized nanoparticles. We report here a systematic investigation on an adenosine aptamer-linked gold nanoparticle system. When the aptamer overhang and the spacer were aligned on the same side, adenosine-responsive disassembly was inhibited. This inhibition effect increased with the length of the spacer, and fully inhibited activity was observed with the spacer containing more than three nucleotides. In contrast to a linear relationship between the spacer length and melting temperature in double-stranded DNA systems without overhangs, the aptamer system displayed a nonlinear relationship, with the melting temperature decreasing exponentially with spacer length. Control experiments suggested that this inhibition effect was due to thermodynamic factors rather than kinetic traps. A comparison with aptamer beacon systems indicated that nanoparticles may play an important role in this inhibition effect, and no specific interactions between the aptamer overhang and spacer were detected. The identity of nucleotides in the spacer did not affect the conclusions. Furthermore, the rate of disassembly or color change was slower at lower temperature or higher ionic strength, but was little affected by pH from 5.2 to 9.2. Therefore, non-base pairing DNA provided another dimension for controlling DNA-linked nanoparticles in addition to pH, temperature, or ionic strength, and this knowledge has resulted in the most optimal construct for sensing applications.

  9. A new interpretation of deformation rates in the Snake River Plain and adjacent basin and range regions based on GPS measurements

    SciTech Connect

    S.J. Payne; R. McCaffrey; R.W. King; S.A. Kattenhorn

    2012-04-01

    We evaluate horizontal Global Positioning System (GPS) velocities together with geologic, volcanic, and seismic data to interpret extension, shear, and contraction within the Snake River Plain and the Northern Basin and Range Province, U.S.A. We estimate horizontal surface velocities using GPS data collected at 385 sites from 1994 to 2009 and present an updated velocity field within the Stable North American Reference Frame (SNARF). Our results show an ENE-oriented extensional strain rate of 5.9 {+-} 0.7 x 10{sup -9} yr{sup -1} in the Centennial Tectonic belt and an E-oriented extensional strain rate of 6.2 {+-} 0.3 x 10{sup -9} yr{sup -1} in the Intermountain Seismic belt combined with the northern Great Basin. These extensional strain rates contrast with the regional north-south contraction of -2.6 {+-} 1.1 x 10{sup -9} yr{sup -1} calculated in the Snake River Plain and Owyhee-Oregon Plateau over a 125 x 650 km region. Tests that include dike-opening reveal that rapid extension by dike intrusion in volcanic rift zones does not occur in the Snake River Plain at present. This slow internal deformation in the Snake River Plain is in contrast to the rapidly-extending adjacent Basin and Range provinces and implies shear along boundaries of the Snake River Plain. We estimate right-lateral shear with slip rates of 0.5-1.5 mm/yr along the northwestern boundary adjacent to the Centennial Tectonic belt and left-lateral oblique extension with slip rates of <0.5 to 1.7 mm/yr along the southeastern boundary adjacent to the Intermountain Seismic belt. The fastest lateral shearing occurs near the Yellowstone Plateau where strike-slip focal mechanisms and faults with observed strike-slip components of motion are documented. The regional GPS velocity gradients are best fit by nearby poles of rotation for the Centennial Tectonic belt, Idaho batholith, Snake River Plain, Owyhee-Oregon Plateau, and central Oregon, indicating that clockwise rotation is driven by extension to the

  10. Correspondence between cluster-ion and bulk solution thermodynamic properties: on the validity of the cluster-pair-based approximation.

    PubMed

    Vlcek, Lukas; Chialvo, Ariel A; Simonson, J Michael

    2013-11-01

    Since the single-ion thermodynamic properties of bulk solutions are not directly accessible from experiments, extrapolations have been devised to estimate them from experimental measurements on small-clusters. Extrapolations based on the cluster-pair-based approximation (CPA) technique (Tissandier et al. J. Phys. Chem. A 1998, 102, 7787-7794) and its variants are currently considered one of the most reliable source of single-ion hydration thermodynamic data and have been used as a benchmark for the development of molecular and continuum solvation models. Despite its importance, the CPA has not been thoroughly tested and recent studies have indicated inconsistencies with molecular simulations. The present work challenges the key CPA assumptions that the hydration properties of single cations and anions in growing clusters rapidly converge to each other following a monotonous trend. Using a combination of simulation techniques to study the transition between alkali halide ions in small clusters and bulk solution, we show that this convergence is rather slow and involves a surprising change in trends, which can result in significant errors in the original estimated single-ion properties. When these cluster-size-dependent effects are taken into account, the inconsistencies between molecular models and experimental predictions disappear, and the value of the proton hydration enthalpy based on the CPA aligns with estimates based on other principles.

  11. Critical Effect of Base Pairing of Target Pyrimidine on the Interstrand Photo-Cross-Linking of DNA via 3-Cyanovinylcarbazole Nucleoside.

    PubMed

    Sakamoto, Takashi; Ooe, Minako; Fujimoto, Kenzo

    2015-08-19

    To evaluate the effect of base pairing of the target pyrimidine on the interstrand photo-cross-linking reaction of DNA via 3-cyanovinylcarbazole nucleoside ((CNV)K), a complementary base of target pyrimidine was substituted with noncanonical purine bases or 1,3-propandiol (S). As the decrease of the hydrogen bonds in the base pairing of target C accelerated the photo-cross-linking reaction markedly (3.6- to 7.7-fold), it can be concluded that the number of hydrogen bonds in the base pairing, i.e., the stability of base pairing, of the target pyrimidine plays a critical role in the interstrand photo-cross-linking reaction. In the case of G to S substitution, the highest photoreactivity toward C was observed, whose photoreaction rate constant (k = 2.0 s(-1)) is comparable to that of (CNV)K toward T paired with A (k = 3.5 s(-1)). This is the most reactive photo-cross-linking reaction toward C in the sequence specific interstrand photo-cross-linking. This might facilitate the design of the photo-cross-linkable oligodeoxyribonucleotides for various target sequences.

  12. Population genetic diversity of the northern snakehead (Channa argus) in China based on the mitochondrial DNA control region and adjacent regions sequences.

    PubMed

    Zhou, Aiguo; Zhuo, Xiaolei; Zou, Qing; Chen, Jintao; Zou, Jixing

    2015-06-01

    Genetic variation and population structure of northern snakehead (Channa argus) from eight locations in China were investigated using mitochondrial DNA control region and adjacent regions sequences. Sequence analysis showed that there were 105 haplotypes in 260 individuals, 48 unique haplotypes and 57 shared haplotypes, but no common haplotype shared by all populations. As a whole, the haplotype diversity was high (h=0.989), while the nucleotide diversity was low (π=0.00482). AMOVA analysis detected significant genetic differentiation among all eight populations (FST=0.328, p<0.01) and 66.17% of the total variance was resulted from intra-population differentiation. UPGMA analysis indicated that the eight populations could be divided into four major clusters, which was consistent with that the eight sampled locations were belonged to four isolated river systems. The neutrality and mismatch distribution tests suggested that the eight populations of C. argus in the sampling locations underwent recent population expansion. Among the eight populations, the Erhai Lake population may represent a unique genetic resource and therefore needs to be conserved. PMID:24724976

  13. Population genetic diversity of the northern snakehead (Channa argus) in China based on the mitochondrial DNA control region and adjacent regions sequences.

    PubMed

    Zhou, Aiguo; Zhuo, Xiaolei; Zou, Qing; Chen, Jintao; Zou, Jixing

    2015-06-01

    Genetic variation and population structure of northern snakehead (Channa argus) from eight locations in China were investigated using mitochondrial DNA control region and adjacent regions sequences. Sequence analysis showed that there were 105 haplotypes in 260 individuals, 48 unique haplotypes and 57 shared haplotypes, but no common haplotype shared by all populations. As a whole, the haplotype diversity was high (h=0.989), while the nucleotide diversity was low (π=0.00482). AMOVA analysis detected significant genetic differentiation among all eight populations (FST=0.328, p<0.01) and 66.17% of the total variance was resulted from intra-population differentiation. UPGMA analysis indicated that the eight populations could be divided into four major clusters, which was consistent with that the eight sampled locations were belonged to four isolated river systems. The neutrality and mismatch distribution tests suggested that the eight populations of C. argus in the sampling locations underwent recent population expansion. Among the eight populations, the Erhai Lake population may represent a unique genetic resource and therefore needs to be conserved.

  14. Mechanism of thermal renaturation and hybridization of nucleic acids: Kramers' process and universality in Watson-Crick base pairing.

    PubMed

    Sikorav, Jean-Louis; Orland, Henri; Braslau, Alan

    2009-03-26

    Renaturation and hybridization reactions lead to the pairing of complementary single-stranded nucleic acids. We present here a theoretical investigation of the mechanism of these reactions in vitro under thermal conditions (dilute solutions of single-stranded chains, in the presence of molar concentrations of monovalent salts and at elevated temperatures). The mechanism follows a Kramers' process, whereby the complementary chains overcome a potential barrier through Brownian motion. The barrier originates from a single rate-limiting nucleation event in which the first complementary base pairs are formed. The reaction then proceeds through a fast growth of the double helix. For the DNA of bacteriophages T7, T4, and phiX174, as well as for Escherichia coli DNA, the bimolecular rate k2 of the reaction increases as a power law of the average degree of polymerization of the reacting single-strands: k2 is proportional to alpha. This relationship holds for 100 < or = < or = 50,000 with an experimentally determined exponent alpha = 0.51 +/- 0.01. The length dependence results from a thermodynamic excluded-volume effect. The reacting single-stranded chains are predicted to be in universal good solvent conditions, and the scaling law is determined by the relevant equilibrium monomer contact probability. The value theoretically predicted for the exponent is alpha = 1 - nutheta2, where nu is Flory's swelling exponent (nu approximately equal 0.588), and theta2 is a critical exponent introduced by des Cloizeaux (theta2 approximately equal 0.82), yielding alpha = 0.52 +/- 0.01, in agreement with the experimental results.

  15. Metal Ion Induced Pairing of Cytosine Bases: Formation of I-Motif Structures Identified by IR Ion Spectroscopy

    NASA Astrophysics Data System (ADS)

    Gao, Juehan; Berden, Giel; Oomens, J.

    2015-06-01

    While the Watson-Crick structure of DNA is among the most well-known molecular structures of our time, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or presence of cations. Pairing of two cytosine (C) bases induced by the sharing of a single proton (C-H^+-C) gives rise to the so-called i-motif, occurring particularly in the telomeric region of DNA, and particularly at low pH. At physiological pH, silver cations were recently suggested to form cytosine dimers in a C-Ag^+-C structure analogous to the hemiprotonated cytosine dimer, which was later confirmed by IR spectroscopy.^1 Here we investigate whether Ag^+ is unique in this behavior. Using infrared action spectroscopy employing the free-electron laser FELIX and a tandem mass spectrometer in combination with quantum-chemical computations, we investigate a series of C-M^+-C complexes, where M is Cu, Li and Na. The complexes are formed by electrospray ionization (ESI) from a solution of cytosine and the metal chloride salt in acetonitrile/water. The complexes of interest are mass-isolated in the cell of a FT ion cyclotron resonance mass spectrometer, where they are irradiated with the tunable IR radiation from FELIX in the 600 - 1800 wn range. Spectra in the H-stretching range are obtained with a LaserVision OPO. Both experimental spectra as well as theoretical calculations indicate that while Cu behaves as Ag, the alkali metal ions induce a clearly different dimer structure, in which the two cytosine units are parallelly displaced. In addition to coordination to the ring nitrogen atom, the alkali metal ions coordinate to the carbonyl oxygen atoms of both cytosine bases, indicating that the alkali metal ion coordination favorably competes with hydrogen bonding between the two cytosine sub-units of the i-motif like structure. 1. Berdakin, Steinmetz, Maitre, Pino, J. Phys. Chem. A 2014, 118, 3804

  16. Epigenetic clustering of lung adenocarcinomas based on DNA methylation profiles in adjacent lung tissue: Its correlation with smoking history and chronic obstructive pulmonary disease.

    PubMed

    Sato, Takashi; Arai, Eri; Kohno, Takashi; Takahashi, Yoriko; Miyata, Sayaka; Tsuta, Koji; Watanabe, Shun-ichi; Soejima, Kenzo; Betsuyaku, Tomoko; Kanai, Yae

    2014-07-15

    The aim of this study was to clarify the significance of DNA methylation alterations during lung carcinogenesis. Infinium assay was performed using 139 paired samples of non-cancerous lung tissue (N) and tumorous tissue (T) from a learning cohort of patients with lung adenocarcinomas (LADCs). Fifty paired N and T samples from a validation cohort were also analyzed. DNA methylation alterations on 1,928 probes occurred in N samples relative to normal lung tissue from patients without primary lung tumors, and were inherited by, or strengthened in, T samples. Unsupervised hierarchical clustering using DNA methylation levels in N samples on all 26,447 probes subclustered patients into Cluster I (n = 32), Cluster II (n = 35) and Cluster III (n = 72). LADCs in Cluster I developed from the inflammatory background in chronic obstructive pulmonary disease (COPD) in heavy smokers and were locally invasive. Most patients in Cluster II were non-smokers and had a favorable outcome. LADCs in Cluster III developed in light smokers were most aggressive (frequently showing lymphatic and blood vessel invasion, lymph node metastasis and an advanced pathological stage), and had a poor outcome. DNA methylation levels of hallmark genes for each cluster, such as IRX2, HOXD8, SPARCL1, RGS5 and EI24, were again correlated with clinicopathological characteristics in the validation cohort. DNA methylation profiles reflecting carcinogenetic factors such as smoking and COPD appear to be established in non-cancerous lung tissue from patients with LADCs and may determine the aggressiveness of tumors developing in individual patients, and thus patient outcome.

  17. Intensified effects of multi-Cu modification on the electronic properties of the modified base pairs containing hetero-ring-expanded pyrimidine bases.

    PubMed

    Lu, Nan; Bu, Yuxiang; Wang, Huatian

    2016-01-28

    Novel DNA base pair derivatives (A2CunU, A2CunC, G3CunU, and G3CunC) are designed by aromatic expansion of pyrimidine bases with four kinds of hetero-rings (denoted by nC and nU, n = 1, 2, 3, and 4) and metal-decoration through Cu replacement of hydrogens in the Watson-Crick hydrogen bond region. Their structures and properties are calculated for examining the cooperative effects of the two modification ways. The calculated results reveal that multiple Cu decoration makes up the deficiencies of size-expansion, and exhibits not only increase of structural stability and reduction of ionization potentials, but also ideal shrink of the HOMO-LUMO gaps, notable enhancement of interbase coupling as well as remarkable redshifts of π → π* transitions for all M-x modified base pairs. The decrease extents of the gaps and ionization potentials follow the same order G3CunU > G3CunC > A2CunU > A2CunC, and in each series (denoted by different n), the gaps, ionization potentials and first π → π* transition energies have an order of 4 < 1 < 2 < 3. The Cu d orbitals function as bridges for π electron delocalization on the conjugated aromatic rings of two bases, leading to an enhancement of transverse electronic communication, as verified by spin density delocalization, orbital composition changes, redshift of the π → π* transition and also advocated by the electron-sharing indexes such as delocalization index, Mayer bond orders and multicenter bonding. Electron localization function ELF-π isosurfaces above the molecular plane further suggested that effective longitudinal conduction is closely relevant with the bicyclic domain involving good electron delocalization and strong π-π stacking between layers. This work presents theoretical evidence for the cooperative effects of metal decoration and ring-expansion modifications on the electronic properties of the modified base pairs and also proves that the base pairs designed here could be competent building blocks for

  18. The tolerance to exchanges of the Watson–Crick base pair in the hammerhead ribozyme core is determined by surrounding elements

    PubMed Central

    Przybilski, Rita; Hammann, Christian

    2007-01-01

    Tertiary interacting elements are important features of functional RNA molecules, for example, in all small nucleolytic ribozymes. The recent crystal structure of a tertiary stabilized type I hammerhead ribozyme revealed a conventional Watson–Crick base pair in the catalytic core, formed between nucleotides C3 and G8. We show that any Watson–Crick base pair between these positions retains cleavage competence in two type III ribozymes. In the Arabidopsis thaliana sequence, only moderate differences in cleavage rates are observed for the different base pairs, while the peach latent mosaic viroid (PLMVd) ribozyme exhibits a preference for a pyrimidine at position 3 and a purine at position 8. To understand these differences, we created a series of chimeric ribozymes in which we swapped sequence elements that surround the catalytic core. The kinetic characterization of the resulting ribozymes revealed that the tertiary interacting loop sequences of the PLMVd ribozyme are sufficient to induce the preference for Y3–R8 base pairs in the A. thaliana hammerhead ribozyme. In contrast to this, only when the entire stem–loops I and II of the A. thaliana sequences are grafted on the PLMVd ribozyme is any Watson–Crick base pair similarly tolerated. The data provide evidence for a complex interplay of secondary and tertiary structure elements that lead, mediated by long-range effects, to an individual modulation of the local structure in the catalytic core of different hammerhead ribozymes. PMID:17666711

  19. Effect of single interstitial impurity in iron-based superconductors with sign-changed s-wave pairing symmetry

    NASA Astrophysics Data System (ADS)

    Yu, Xiang-Long; Liu, Da-Yong; Quan, Ya-Min; Zheng, Xiao-Jun; Zou, Liang-Jian

    2015-12-01

    We employ the self-consistent Bogoliubov-de Gennes (BdG) formulation to investigate the effect of single interstitial nonmagnetic/magnetic impurity in iron-based superconductors with s ± -wave pairing symmetry. We find that both the nonmagnetic and magnetic impurities can induce bound states within the superconducting (SC) gap and a π phase shift of SC order parameter at the impurity site. However, different from the interstitial-nonmagnetic-impurity case characterized by two symmetric peaks with respect to zero energy, the interstitial magnetic one only induces single bound-state peak. In the strong scattering regime this peak can appear at the Fermi level, which has been observed in the recent scanning tunneling microscope (STM) experiment of Fe(Te,Se) superconductor with interstitial Fe impurities (Yin et al. 2015 [44]). This novel single in-gap peak feature also distinguishes the interstitial case from the substitutional one with two peaks. These results provide important information for comparing the different impurity effects in the iron-based superconductors.

  20. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.

    PubMed

    Hasan, Md Mehedi; Zhou, Yuan; Lu, Xiaotian; Li, Jinyan; Song, Jiangning; Zhang, Ziding

    2015-01-01

    Prokaryotic proteins are regulated by pupylation, a type of post-translational modification that contributes to cellular function in bacterial organisms. In pupylation process, the prokaryotic ubiquitin-like protein (Pup) tagging is functionally analogous to ubiquitination in order to tag target proteins for proteasomal degradation. To date, several experimental methods have been developed to identify pupylated proteins and their pupylation sites, but these experimental methods are generally laborious and costly. Therefore, computational methods that can accurately predict potential pupylation sites based on protein sequence information are highly desirable. In this paper, a novel predictor termed as pbPUP has been developed for accurate prediction of pupylation sites. In particular, a sophisticated sequence encoding scheme [i.e. the profile-based composition of k-spaced amino acid pairs (pbCKSAAP)] is used to represent the sequence patterns and evolutionary information of the sequence fragments surrounding pupylation sites. Then, a Support Vector Machine (SVM) classifier is trained using the pbCKSAAP encoding scheme. The final pbPUP predictor achieves an AUC value of 0.849 in 10-fold cross-validation tests and outperforms other existing predictors on a comprehensive independent test dataset. The proposed method is anticipated to be a helpful computational resource for the prediction of pupylation sites. The web server and curated datasets in this study are freely available at http://protein.cau.edu.cn/pbPUP/.

  1. Design of A 5-Bit Fully Parallel Analog to Digital Converter Using Common Gate Differrential Mos Pair-Based Comparator

    NASA Astrophysics Data System (ADS)

    Aytar, Oktay

    2015-09-01

    This paper presents a novel comparator structure based on the common gate differential MOS pair. The proposed comparator has been applied to fully parallel analog to digital converter (A/D converter). Furthermore, this article presents 5 bit fully parallel A/D Converter design using the cadence IC5141 design platform and NCSU(North Carolina State University) design kit with 0.18 μm CMOS technology library. The proposed fully parallel A/D converter consist of resistor array block, comparator block, 1-n decoder block and programmable logic array. The 1-n decoder block includes latch block and thermometer code circuit that is implemented using transmission gate based multiplexer circuit. Thus, sampling frequency and analog bandwidth are increased. The INL and DNL of the proposed fully parallel A/D converter are (0/ + 0.63) LSB and (-0.26/ + 0.31) LSB at a sampling frequency of 5 GS/s with an input signal of 50 MHz, respectively. The proposed fully parallel A/D Converter consumes 340 mW from 1.8 V supply.

  2. Monitoring of dual bio-molecular events using FRET biosensors based on mTagBFP/sfGFP and mVenus/mKOκ fluorescent protein pairs.

    PubMed

    Su, Ting; Pan, Shaotao; Luo, Qingming; Zhang, Zhihong

    2013-08-15

    Fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are powerful tools for dynamically measuring cellular molecular events because they offer high spatial and temporal resolution in living cells. Despite the broad use of FP-based FRET biosensors in cell biology, imaging of multiple molecular events (multi-parameter molecular imaging) in single cells using current FRET pairs remains difficult because it usually requires a control group for additional data calibration. Hence, spectrally compatible FRET pairs that do not require complex image calibration are the key to widespread applications of FP-based FRET biosensors in multi-parameter molecular imaging. Here, we report a new combination of spectrally distinguishable FRET pairs for dual-parameter molecular imaging: mTagBFP/sfGFP (blue and green FP, B/G) and mVenus/mKOκ (yellow and orange FP, Y/O). We demonstrate that additional image correction is not necessary for these dual FRET pairs. Using these dual FRET pairs, we achieve simultaneous imaging of Src and Ca(2+) signaling in single living cells stimulated with epithelial growth factor (EGF). By converting traditional FRET biosensors into B/G and Y/O-based biosensors, additional applications are available to elucidate the dynamic relationships of multiple molecular events within a single living cell.

  3. Excited state properties of naphtho-homologated xxDNA bases and effect of methanol solution, deoxyribose, and base pairing.

    PubMed

    Zhang, Laibin; Ren, Tingqi; Tian, Jianxiang; Yang, Xiuqin; Zhou, Liuzhu; Li, Xiaoming

    2013-04-18

    Design and synthesis of fluorescent nucleobase analogues for studying structures and dynamics of nucleic acids have attracted much attention in recent years. In the present work, a comprehensive theoretical study of electronic transitions of naphtho-homologated base analogues, namely, xxC, xxT, xxA, and xxG, was performed. The nature of the low-lying excited states was discussed, and the results were compared with those of x-bases. Geometrical characteristics of the lowest excited singlet ππ* states were explored using the CIS method. The calculated excitation maxima are 423, 397, 383, and 357 nm for xxA, xxG, xxC, and xxT, respectively, and they are greatly red-shifted compared with x-bases and natural bases, allowing them to be selectively excited in the presence of the natural bases. In the gas phase, the fluorescence from them would be expected to occur around 497, 461, 457, and 417 nm, respectively. The effects of methanol solution, deoxyribose, and base paring with their complementary natural bases on the relevant absorption and emission spectra of these modified bases were also examined.

  4. View from water showing south facade and adjacent boat slips ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View from water showing south facade and adjacent boat slips (Facility Nos. S375 & S376) - U.S. Naval Base, Pearl Harbor, Boat House, Hornet Avenue at Independence Street, Pearl City, Honolulu County, HI

  5. OBLIQUE OF SOUTHWEST END AND SOUTHEAST SIDE, WITH ADJACENT FACILITY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    OBLIQUE OF SOUTHWEST END AND SOUTHEAST SIDE, WITH ADJACENT FACILITY 391 IN THE FOREGROUND. - U.S. Naval Base, Pearl Harbor, Joint Intelligence Center, Makalapa Drive in Makalapa Administration Area, Pearl City, Honolulu County, HI

  6. VIEW OF LAMP FIXTURE (EXTERIOR) ADJACENT TO ENTRANCE AT SOUTHWEST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW OF LAMP FIXTURE (EXTERIOR) ADJACENT TO ENTRANCE AT SOUTHWEST CORNER OF BUILDING 23, FACING NORTH - Roosevelt Base, Auditorium-Gymnasium, West Virginia Street between Richardson & Reeves Avenues, Long Beach, Los Angeles County, CA

  7. VIEW OF NORTHERN AND EASTERN SIDES FROM PARKING LOT ADJACENT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW OF NORTHERN AND EASTERN SIDES FROM PARKING LOT ADJACENT TO BUILDING 199 (POLICE STATION) - U.S. Naval Base, Pearl Harbor, Post Office, Avenue A near Eleventh Avenue, Pearl City, Honolulu County, HI

  8. Basement, room 23, looking southwest into two adjacent offices with ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Basement, room 23, looking southwest into two adjacent offices with soundproof walls and pedestal flooring - March Air Force Base, Strategic Air Command, Combat Operations Center, 5220 Riverside Drive, Moreno Valley, Riverside County, CA

  9. High yield and ultrafast sources of electrically triggered entangled-photon pairs based on strain-tunable quantum dots

    NASA Astrophysics Data System (ADS)

    Zhang, Jiaxiang; Wildmann, Johannes S.; Ding, Fei; Trotta, Rinaldo; Huo, Yongheng; Zallo, Eugenio; Huber, Daniel; Rastelli, Armando; Schmidt, Oliver G.

    2015-12-01

    Triggered sources of entangled photon pairs are key components in most quantum communication protocols. For practical quantum applications, electrical triggering would allow the realization of compact and deterministic sources of entangled photons. Entangled-light-emitting-diodes based on semiconductor quantum dots are among the most promising sources that can potentially address this task. However, entangled-light-emitting-diodes are plagued by a source of randomness, which results in a very low probability of finding quantum dots with sufficiently small fine structure splitting for entangled-photon generation (~10-2). Here we introduce strain-tunable entangled-light-emitting-diodes that exploit piezoelectric-induced strains to tune quantum dots for entangled-photon generation. We demonstrate that up to 30% of the quantum dots in strain-tunable entangled-light-emitting-diodes emit polarization-entangled photons. An entanglement fidelity as high as 0.83 is achieved with fast temporal post selection. Driven at high speed, that is 400 MHz, strain-tunable entangled-light-emitting-diodes emerge as promising devices for high data-rate quantum applications.

  10. Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex.

    PubMed

    Loth, Karine; Landon, Céline; Paquet, Françoise

    2015-04-01

    MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55 in laboratory growth conditions and is structurally unrelated to other DNA-binding proteins. MC1 functions are to shape and to protect DNA against thermal denaturation by binding to it. Therefore, MC1 has a strong affinity for any double-stranded DNA. However, it recognizes and preferentially binds to bent DNA, such as four-way junctions and negatively supercoiled DNA minicircles. Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. We present here the NMR chemical shifts assignments of each partner in the complex, (1)H (15)N MC1 protein and (1)H (13)C (15)N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex.

  11. Representation of multi-target activity landscapes through target pair-based compound encoding in self-organizing maps.

    PubMed

    Iyer, Preeti; Bajorath, Jürgen

    2011-11-01

    Activity landscape representations provide access to structure-activity relationships information in compound data sets. In general, activity landscape models integrate molecular similarity relationships with biological activity data. Typically, activity against a single target is monitored. However, for steadily increasing numbers of compounds, activity against multiple targets is reported, resulting in an opportunity, and often a need, to explore multi-target structure-activity relationships. It would be attractive to utilize activity landscape representations to aid in this process, but the design of activity landscapes for multiple targets is a complicated task. Only recently has a first multi-target landscape model been introduced, consisting of an annotated compound network focused on the systematic detection of activity cliffs. Herein, we report a conceptually different multi-target activity landscape design that is based on a 2D projection of chemical reference space using self-organizing maps and encodes compounds as arrays of pair-wise target activity relationships. In this context, we introduce the concept of discontinuity in multi-target activity space. The well-ordered activity landscape model highlights centers of discontinuity in activity space and is straightforward to interpret. It has been applied to analyze compound data sets with three, four, and five target annotations and identify multi-target structure-activity relationships determinants in analog series.

  12. Spectrophotometric Determination of Cefixime Trihydrate in Pharmaceutical Formulations Based on Ion-Pair Reaction with Bromophenol Blue.

    PubMed

    Keskar, Mrudul R; Jugade, Ravin M

    2015-01-01

    Cefixime trihydrate is a broad spectrum cephalosporin antibiotic, effective against gram-positive and gram-negative bacterial infections. Simple and rapid method has been developed for the determination of cefixime trihydrate in bulk and pharmaceutical formulations. This method was based on the formation of bluish-green ion-pair complex of cefixime trihydrate with bromophenol blue in dimethyl sulfoxide (DMSO)-acetonitrile medium. Different parameters were studied and optimized. A 2:1 complex was formed between the drug and reagent almost instantaneously at room temperature which has λmax of 610 nm. Under optimum conditions, calibration curve was found to be linear over the range of 10-130 μg mL(-1). The method was subjected to analytical quality control. The limit of detection was found to be 1.08 μg mL(-1). Recovery studies and interference studies were carried out. The proposed method was successfully applied to the determination of cefixime trihydrate in bulk and pharmaceutical formulations with high precision and accuracy.

  13. High yield and ultrafast sources of electrically triggered entangled-photon pairs based on strain-tunable quantum dots.

    PubMed

    Zhang, Jiaxiang; Wildmann, Johannes S; Ding, Fei; Trotta, Rinaldo; Huo, Yongheng; Zallo, Eugenio; Huber, Daniel; Rastelli, Armando; Schmidt, Oliver G

    2015-01-01

    Triggered sources of entangled photon pairs are key components in most quantum communication protocols. For practical quantum applications, electrical triggering would allow the realization of compact and deterministic sources of entangled photons. Entangled-light-emitting-diodes based on semiconductor quantum dots are among the most promising sources that can potentially address this task. However, entangled-light-emitting-diodes are plagued by a source of randomness, which results in a very low probability of finding quantum dots with sufficiently small fine structure splitting for entangled-photon generation (∼10(-2)). Here we introduce strain-tunable entangled-light-emitting-diodes that exploit piezoelectric-induced strains to tune quantum dots for entangled-photon generation. We demonstrate that up to 30% of the quantum dots in strain-tunable entangled-light-emitting-diodes emit polarization-entangled photons. An entanglement fidelity as high as 0.83 is achieved with fast temporal post selection. Driven at high speed, that is 400 MHz, strain-tunable entangled-light-emitting-diodes emerge as promising devices for high data-rate quantum applications.

  14. Isolation breeds naivety: island living robs Australian varanid lizards of toad-toxin immunity via four-base-pair mutation.

    PubMed

    Ujvari, Beata; Mun, Hee-chang; Conigrave, Arthur D; Bray, Alessandra; Osterkamp, Jens; Halling, Petter; Madsen, Thomas

    2013-01-01

    Since their introduction to the toad-free Australian continent cane toads (Bufo marinus) have caused a dramatic increase in naïve varanid mortality when these large lizards attempt to feed on this toxic amphibian. In contrast Asian-African varanids, which have coevolved with toads, are resistant to toad toxin. Toad toxins, such as Bufalin target the H1-H2 domain of the α(1) subunit of the sodium-potassium-ATPase enzyme. Sequencing of this domain revealed identical nucleotide sequences in four Asian as well as in three African varanids, and identical sequences in all 11 Australian varanids. However, compared to the Asian-African varanids, the Australian varanids showed four-base-pair substitutions, resulting in the alteration in three of the 12 amino acids representing the H1-H2 domain. The phenotypic effect of the substitutions was investigated in human embryonic kidney (HEK) 293 cells stably transfected with the Australian and the Asian-African H1-H2 domains. The transfections resulted in an approximate 3000-fold reduction in resistance to Bufalin in the Australian HEK293 cells compared to the Asian-African HEK293 cells, demonstrating the critical role of this minor mutation in providing Bufalin resistance. Our study hence presents a clear link between genotype and phenotype, a critical step in understanding the evolution of phenotypic diversity.

  15. High yield and ultrafast sources of electrically triggered entangled-photon pairs based on strain-tunable quantum dots

    PubMed Central

    Zhang, Jiaxiang; Wildmann, Johannes S.; Ding, Fei; Trotta, Rinaldo; Huo, Yongheng; Zallo, Eugenio; Huber, Daniel; Rastelli, Armando; Schmidt, Oliver G.

    2015-01-01

    Triggered sources of entangled photon pairs are key components in most quantum communication protocols. For practical quantum applications, electrical triggering would allow the realization of compact and deterministic sources of entangled photons. Entangled-light-emitting-diodes based on semiconductor quantum dots are among the most promising sources that can potentially address this task. However, entangled-light-emitting-diodes are plagued by a source of randomness, which results in a very low probability of finding quantum dots with sufficiently small fine structure splitting for entangled-photon generation (∼10−2). Here we introduce strain-tunable entangled-light-emitting-diodes that exploit piezoelectric-induced strains to tune quantum dots for entangled-photon generation. We demonstrate that up to 30% of the quantum dots in strain-tunable entangled-light-emitting-diodes emit polarization-entangled photons. An entanglement fidelity as high as 0.83 is achieved with fast temporal post selection. Driven at high speed, that is 400 MHz, strain-tunable entangled-light-emitting-diodes emerge as promising devices for high data-rate quantum applications. PMID:26621073

  16. Can copper(II) mediate Hoogsteen base-pairing in a left-handed DNA duplex? A pulse EPR study.

    PubMed

    Santangelo, Maria Grazia; Antoni, Philipp M; Spingler, Bernhard; Jeschke, Gunnar

    2010-02-22

    Pulse EPR spectroscopy is used to investigate possible structural features of the copper(II) ion coordinated to poly(dG-dC).poly(dG-dC) in a frozen aqueous solution, and the structural changes of the polynucleotide induced by the presence of the metal ion. Two different copper species were identified and their geometry explained by a molecular model. According to this model, one species is exclusively coordinated to a single guanine with the N7 nitrogen atom forming a coordinative bond with the copper. In the other species, a guanine and a cytosine form a ternary complex together with the copper ion. A copper crosslink between the N7 of guanine and N3 of cytosine is proposed as the most probable coordination site. Moreover, no evidence was found for an interaction of either copper species with a phosphate group or equatorial water molecules. In addition, circular dichroism (CD) spectroscopy showed that the DNA of the Cu(II)-poly(dG-dC).poly(dG-dC) adducts resembles the left-handed Z-form. These results suggest that metal-mediated Hoogsteen base pairing, as previously proposed for a right-handed DNA duplex, can also occur in a double-stranded left-handed DNA.

  17. Theoretical study on absorption and emission spectra of size-expanded Janus-type AT nucleobases and effect of base pairing.

    PubMed

    Liu, Hongxia; Song, Qixia; Liu, Jianhua; Li, Yan; Wang, Haijun

    2014-01-01

    Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we design benzo- and naphtha-expanded Janus AT base analogues, using DFT, TDDFT, and CIS methods to investigate the structural and optical properties of the Janus AT base analogues (termed as J-AT, xJ-AT, yyJ-AT, BF, xBF and yyBF), and also consider the effect of base pairing. The results show that the Janus AT base analogues can pair with T and A simultaneously to form stable H-bonded WC base pairs. The ground state structure of J-AT is similar to BF, the size expansion is 2.42Å for the x-Janus AT bases and 4.86Å for the yy-Janus AT bases. The excited state geometries of J-AT and BF change dramatically, while the other bases are similar to the ground state geometries. The lowest excited singlet transitions of the Janus AT base analogues are predicted to be of ππ(*) character and mainly dominated by the configuration HOMO-LUMO. The maximum absorption wavelengths of size expansion Janus AT base analogues are greatly red shifted compared with J-AT (or BF). BF, xBF and yyJ-AT have larger oscillator strengths than J-AT, xJ-AT and yyBF. The emission wavelengths of the Janus AT base analogues also exhibit red shifts from x-Janus AT bases to yy-Janus AT bases. However, the emission wavelengths of J-AT and BF change greatly, which are coincident with the structures observed in the excited state geometries. With regard to the WC base pairs, the B3LYP functional reveals that the lowest energy transitions of some base pairs are charge transfer excitation, while the other base pairs are local excitation. The CAM-B3LYP functional predicts that all the lowest transitions are localized on the Janus AT bases, and show good agreement with the results of the M062X functional. PMID:24368287

  18. Theoretical study on absorption and emission spectra of size-expanded Janus-type AT nucleobases and effect of base pairing

    NASA Astrophysics Data System (ADS)

    Liu, Hongxia; Song, Qixia; Liu, Jianhua; Li, Yan; Wang, Haijun

    2014-03-01

    Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we design benzo- and naphtha-expanded Janus AT base analogues, using DFT, TDDFT, and CIS methods to investigate the structural and optical properties of the Janus AT base analogues (termed as J-AT, xJ-AT, yyJ-AT, BF, xBF and yyBF), and also consider the effect of base pairing. The results show that the Janus AT base analogues can pair with T and A simultaneously to form stable H-bonded WC base pairs. The ground state structure of J-AT is similar to BF, the size expansion is 2.42 Å for the x-Janus AT bases and 4.86 Å for the yy-Janus AT bases. The excited state geometries of J-AT and BF change dramatically, while the other bases are similar to the ground state geometries. The lowest excited singlet transitions of the Janus AT base analogues are predicted to be of ππ* character and mainly dominated by the configuration HOMO-LUMO. The maximum absorption wavelengths of size expansion Janus AT base analogues are greatly red shifted compared with J-AT (or BF). BF, xBF and yyJ-AT have larger oscillator strengths than J-AT, xJ-AT and yyBF. The emission wavelengths of the Janus AT base analogues also exhibit red shifts from x-Janus AT bases to yy-Janus AT bases. However, the emission wavelengths of J-AT and BF change greatly, which are coincident with the structures observed in the excited state geometries. With regard to the WC base pairs, the B3LYP functional reveals that the lowest energy transitions of some base pairs are charge transfer excitation, while the other base pairs are local excitation. The CAM-B3LYP functional predicts that all the lowest transitions are localized on the Janus AT bases, and show good agreement with the results of the M062X functional.

  19. Pairing Learners in Pair Work Activity

    ERIC Educational Resources Information Center

    Storch, Neomy; Aldosari, Ali

    2013-01-01

    Although pair work is advocated by major theories of second language (L2) learning and research findings suggest that pair work facilitates L2 learning, what is unclear is how to best pair students in L2 classes of mixed L2 proficiency. This study investigated the nature of pair work in an English as a Foreign Language (EFL) class in a college in…

  20. Design of two and three input molecular logic gates using non-Watson-Crick base pairing-based molecular beacons.

    PubMed

    Lin, Jia-Hui; Tseng, Wei-Lung

    2014-03-21

    This study presents a single, resettable, and sensitive molecular beacon (MB) used to operate molecular-scale logic gates. The MB consists of a random DNA sequence, a fluorophore at the 5'-end, and a quencher at the 3'-end. The presence of Hg(2+), Ag(+), and coralyne promoted the formation of stable T-Hg(2+)-T, C-Ag(+)-C, and A2-coralyne-A2 coordination in the MB probe, respectively, thereby driving its conformational change. The metal ion or small molecule-mediated coordination of mismatched DNA brought the fluorophore and the quencher into close proximity, resulting in collisional quenching of fluorescence between the two organic dyes. Because thiol can bind Hg(2+) and remove it from the T-Hg(2+)-T-based MB, adding thiol to a solution of the T-Hg(2+)-T-based MB allowed the fluorophore and the quencher to be widely separated. A similar phenomenon was observed when replacing Hg(2+) with Ag(+). Because Ag(+) strongly binds to iodide, cyanide, and cysteine, they were capable of removing Ag(+) from the C-Ag(+)-C-based MB, restoring the fluorescence of the MB. Moreover, the fluorescence of the A2-coralyne-A2-based MB could be switched on by adding polyadenosine. Using these analytes as inputs and the MB as a signal transducer, we successfully developed a series of two-input, three-input, and set-reset logic gates at the molecular level.

  1. Modified normal-phase ion-pair chromatographic methods for the facile separation and purification of imidazolium-based ionic compounds

    SciTech Connect

    Urban, ND; Schenkel, MR; Robertson, LA; Noble, RD; Gin, DL

    2012-07-04

    lmidazolium- and oligo(imidazolium)-based ionic organic compounds are important in the design of room-temperature ionic liquid materials; however, the chromatographic analysis and separation of such compounds are often difficult. A convenient and inexpensive method for effective thin-layer chromatography (TLC) analysis and column chromatography separation of imidazolium-based ionic compounds is presented. Normal-phase ion-pair TLC is used to effectively analyze homologous mixtures of these ionic compounds. Subsequent separation of the mixtures is performed using ion-pair flash chromatography on normal-phase silica gel, yielding high levels of recovery. This method also results in a complete exchange of the counter anion on the imidazolium compounds to the anion of the ion-pair reagent. (C) 2012 Elsevier Ltd. All rights reserved.

  2. Prospective very young asteroid pairs

    NASA Astrophysics Data System (ADS)

    Galád, A.; Vokrouhlický, D.; Zizka, J.

    2014-07-01

    Several tens of asteroid pairs can be discerned from the background main-belt asteroids. The majority of them are thought to have formed within only the last few 10^6 yr. The youngest recognized pairs have formed more than ≈ 10 kyr ago. As some details of pair formation are still not understood well, the study of young pairs is of great importance. It is mainly because the conditions at the time of the pair formation could be deduced much more reliably for young pairs. For example, space weathering on the surfaces of the components, or changes in their rotational properties (in spin rates, tumbling, coordinates of rotational pole) could be negligible since the formation of young pairs. Also, possible strong perturbations by main-belt bodies on pair formation can be reliably studied only for extremely young pairs. Some pairs can quickly blend in with the background asteroids, so even the frequency of asteroid pair formation could be determined more reliably based on young pairs (though only after a statistically significant sample is at disposal). In our regular search for young pairs in the growing asteroid database, only multiopposition asteroids with very similar orbital and proper elements are investigated. Every pair component is represented by a number of clones within orbital uncertainties and drifting in semimajor axis due to the Yarkovsky effect. We found that, if the previously unrecognized pairs (87887) 2000 SS_{286} - 2002 AT_{49} and (355258) 2007 LY_{4} - 2013AF_{40} formed at the recent very close approach of their components, they could become the youngest known pairs. In both cases, the relative encounter velocities of the components were only ˜ 0.1 m s^{-1}. However, the minimum distances between some clones are too large and a few clones of the latter pair did not encounter recently (within ≈ 10 kyr). The age of some prospective young pairs cannot be determined reliably without improved orbital properties (e.g., the second component of a pair

  3. Young Learners' Interactional Development in Task-Based Paired-Assessment in Their First and Foreign Languages: A Case of English Learners in China

    ERIC Educational Resources Information Center

    Butler, Yuko Goto; Zeng, Wei

    2015-01-01

    In response to the growing interest in evaluating young learners' foreign language (FL) performance, this study aims to deepen our understanding of young learners' developmental differences in interaction during task-based paired-language assessments. To examine age effects separately from the effect of general language proficiency, we analysed…

  4. Influence of the incorporation of (S)-9-(3,4-dihydroxybutyl)adenine on the enzymatic stability and base-pairing properties of oligodeoxynucleotides.

    PubMed Central

    Augustyns, K; Van Aerschot, A; Van Schepdael, A; Urbanke, C; Herdewijn, P

    1991-01-01

    (S)-9-(3,4-dihydroxybutyl)adenine was used at several positions as nucleoside substitute in the synthesis of dimers and 13-mers. Therefore we used the phosporamidite and the H-phosphonate chemistry. The nuclease susceptibilities and the base-pairing properties of these oligomers have been evaluated. PMID:2041735

  5. Resistance of human cytomegalovirus to cyclopropavir maps to a base pair deletion in the open reading frame of UL97.

    PubMed

    Gentry, Brian G; Vollmer, Laura E; Hall, Ellie D; Borysko, Katherine Z; Zemlicka, Jiri; Kamil, Jeremy P; Drach, John C

    2013-09-01

    Human cytomegalovirus (HCMV) is a widespread pathogen in the human population, affecting many immunologically immature and immunocompromised patients, and can result in severe complications, such as interstitial pneumonia and mental retardation. Current chemotherapies for the treatment of HCMV infections include ganciclovir (GCV), foscarnet, and cidofovir. However, the high incidences of adverse effects (neutropenia and nephrotoxicity) limit the use of these drugs. Cyclopropavir (CPV), a guanosine nucleoside analog, is 10-fold more active against HCMV than GCV (50% effective concentrations [EC50s] = 0.46 and 4.1 μM, respectively). We hypothesize that the mechanism of action of CPV is similar to that of GCV: phosphorylation to a monophosphate by viral pUL97 protein kinase with further phosphorylation to a triphosphate by endogenous kinases, resulting in inhibition of viral DNA synthesis. To test this hypothesis, we isolated a CPV-resistant virus, sequenced its genome, and discovered that bp 498 of UL97 was deleted. This mutation caused a frameshift in UL97 resulting in a truncated protein that lacks a kinase domain. To determine if this base pair deletion was responsible for drug resistance, the mutation was engineered into the wild-type viral genome, which was then exposed to increasing concentrations of CPV. The results demonstrate that the engineered virus was approximately 72-fold more resistant to CPV (EC50 = 25.8 ± 3.1 μM) than the wild-type virus (EC50 = 0.36 ± 0.11 μM). We conclude, therefore, that this mutation is sufficient for drug resistance and that pUL97 is involved in the mechanism of action of CPV.

  6. Oxygen-aromatic contacts in intra-strand base pairs: analysis of high-resolution DNA crystal structures and quantum chemical calculations.

    PubMed

    Jain, Alok; Krishna Deepak, R N V; Sankararamakrishnan, Ramasubbu

    2014-07-01

    Three-dimensional structures of biomolecules are stabilized by a large number of non-covalent interactions and some of them such as van der Waals, electrostatic and hydrogen bond interactions are well characterized. Delocalized π-electron clouds of aromatic residues are known to be involved in cation-π, CH-π, OH-π and π-π interactions. In proteins, many examples have been found in which the backbone carbonyl oxygen of one residue makes close contact with the aromatic center of aromatic residues. Quantum chemical calculations suggest that such contacts may provide stability to the protein secondary structures. In this study, we have systematically analyzed the experimentally determined high-resolution DNA crystal structures and identified 91 examples in which the aromatic center of one base is in close contact (<3.5Ǻ) with the oxygen atom of preceding (Group-I) or succeeding base (Group-II). Examples from Group-I are overwhelmingly observed and cytosine or thymine is the preferred base contributing oxygen atom in Group-I base pairs. A similar analysis of high-resolution RNA structures surprisingly did not yield many examples of oxygen-aromatic contact of similar type between bases. Ab initio quantum chemical calculations on compounds based on DNA crystal structures and model compounds show that interactions between the bases in base pairs with oxygen-aromatic contacts are energetically favorable. Decomposition of interaction energies indicates that dispersion forces are the major cause for energetically stable interaction in these base pairs. We speculate that oxygen-aromatic contacts in intra-strand base pairs in a DNA structure may have biological significance.

  7. 2012 IUPAP C10 Young Scientist Prize on the Structure and Dynamics of Condensed Matter Lecture: Spin Fluctuations and Pairing in Fe-based Superconductors

    NASA Astrophysics Data System (ADS)

    Christianson, A. D.

    2012-02-01

    The origin of superconductivity in the Fe-based superconductors, like that in other unconventional superconductors, remains shrouded in mystery. How the pairing bosons emerge either due to or in spite of the strong magnetic interactions found in the Fe-based superconductors is one of the most thoroughly investigated questions in the field. A prominent example of the interplay of superconductivity and magnetism is the dramatic shift of spectral weight from the low energy spin excitations to an energy which is related to the superconducting gap resulting in a peak in the spin excitation spectrum localized in both momentum and energy which occurs at the onset of superconductivity. The appearance of the new peak in the spin excitation spectrum below the superconducting transition temperature is referred to as s spin resonance and is most commonly interpreted as indicating a sign change of the superconducting order parameter on different portions of the Fermi surface and thus is consistent with an extended s-wave or s± pairing symmetry in many Fe-based superconductors. We will review the observations and implications of the spin resonance across the Fe-based superconductors. In particular we will examine the relationship between the resonance energy and the superconducting transition temperature as a function of chemical doping and pressure. While the spin resonance provides important information about pairing symmetry, there does not appear to be sufficient spectral to explain the pairing strength. Thus the remainder of the spin excitation spectrum must be examined to determine if spin fluctuations are ultimately responsible for pairing in the Fe-based materials. Consequently, we will discuss in detail the way in which the spin excitations evolve from the nonsuperconducting compounds to their superconducting relatives as a function of chemical doping.

  8. Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2;#8242;-deoxyadenosine:dT Base Pairing in DNA

    SciTech Connect

    Kowal, Ewa A.; Ganguly, Manjori; Pallan, Pradeep S.; Marky, Luis A.; Gold, Barry; Egli, Martin; Stone, Michael P.

    2012-02-15

    As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2'-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson-Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C-H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 {angstrom} resolution in the presence of Mg{sup 2+}. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry and the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA.

  9. Robustness of s-wave pairing symmetry in iron-based superconductors and its implications for fundamentals of magnetically driven high-temperature superconductivity

    NASA Astrophysics Data System (ADS)

    Hu, Jiangping; Yuan, Jing

    2016-10-01

    Based on the assumption that the superconducting state belongs to a single irreducible representation of lattice symmetry, we propose that the pairing symmetry in all measured iron-based superconductors is generally consistent with the A 1 g s-wave. Robust s-wave pairing throughout the different families of iron-based superconductors at different doping regions signals two fundamental principles behind high- T c superconducting mechanisms: (i) the correspondence principle: the short-range magnetic-exchange interactions and the Fermi surfaces act collaboratively to achieve high- T c superconductivity and determine pairing symmetries; (ii) the magnetic-selection pairing rule: superconductivity is only induced by the magnetic-exchange couplings from the super-exchange mechanism through cation-anion-cation chemical bonding. These principles explain why unconventional high- T c superconductivity appears to be such a rare but robust phenomena, with its strict requirements regarding the electronic environment. The results will help us to identify new electronic structures that can support high- T c superconductivity.

  10. Silver Ions in Non-canonical DNA Base Pairs: Metal-Mediated Mismatch Stabilization of 2'-Deoxyadenosine and 7-Deazapurine Derivatives with 2'-Deoxycytidine and 2'-Deoxyguanosine.

    PubMed

    Yang, Haozhe; Seela, Frank

    2016-09-01

    Novel silver-mediated dA-dC, dA*-dC, and dA*-dG base pairs were formed in a natural DNA double helix environment (dA* denotes 7-deaza-dA, 7-deaza-7-iodo-dA, and 7-cyclopropyl-7-deaza-dA). 7-Deazapurine nucleosides enforce silver ion binding and direct metal-mediated base pair formation to their Watson-Crick face. New phosphoramidites were prepared from 7-deaza-dA, 7-deaza-7-iodo-dA, and 7-cyclopropyl-7-deaza-dA, which contain labile isobutyryl protecting groups. Solid-phase synthesis furnished oligonucleotides that contain mismatches in near central positions. Increased thermal stabilities (higher Tm values) were observed for oligonucleotide duplexes with non-canonical dA*-dC and dA-dC pairs in the presence of silver ions. The stability of the silver-mediated base pairs was pH dependent. Silver ion binding was not observed for the dA-dG mismatch but took place when mismatches were formed between 7-deazaadenine and guanine. The specific binding of silver ions was confirmed by stoichiometric UV titration experiments, which proved that one silver ion is captured by one mismatch. The stability increase of canonical DNA mismatches might have an impact on cellular DNA repair. PMID:27492501

  11. Systematic exploration of a class of hydrophobic unnatural base pairs yields multiple new candidates for the expansion of the genetic alphabet.

    PubMed

    Dhami, Kirandeep; Malyshev, Denis A; Ordoukhanian, Phillip; Kubelka, Tomáš; Hocek, Michal; Romesberg, Floyd E

    2014-01-01

    We have developed a family of unnatural base pairs (UBPs), which rely on hydrophobic and packing interactions for pairing and which are well replicated and transcribed. While the pair formed between d5SICS and dNaM (d5SICS-dNaM) has received the most attention, and has been used to expand the genetic alphabet of a living organism, recent efforts have identified dTPT3-dNaM, which is replicated with even higher fidelity. These efforts also resulted in more UBPs than could be independently analyzed, and thus we now report a PCR-based screen to identify the most promising. While we found that dTPT3-dNaM is generally the most promising UBP, we identified several others that are replicated nearly as well and significantly better than d5SICS-dNaM, and are thus viable candidates for the expansion of the genetic alphabet of a living organism. Moreover, the results suggest that continued optimization should be possible, and that the putatively essential hydrogen-bond acceptor at the position ortho to the glycosidic linkage may not be required. These results clearly demonstrate the generality of hydrophobic forces for the control of base pairing within DNA, provide a wealth of new structure-activity relationship data and importantly identify multiple new candidates for in vivo evaluation and further optimization.

  12. Systematic exploration of a class of hydrophobic unnatural base pairs yields multiple new candidates for the expansion of the genetic alphabet

    PubMed Central

    Dhami, Kirandeep; Malyshev, Denis A.; Ordoukhanian, Phillip; Kubelka, Tomáš; Hocek, Michal; Romesberg, Floyd E.

    2014-01-01

    We have developed a family of unnatural base pairs (UBPs), which rely on hydrophobic and packing interactions for pairing and which are well replicated and transcribed. While the pair formed between d5SICS and dNaM (d5SICS-dNaM) has received the most attention, and has been used to expand the genetic alphabet of a living organism, recent efforts have identified dTPT3-dNaM, which is replicated with even higher fidelity. These efforts also resulted in more UBPs than could be independently analyzed, and thus we now report a PCR-based screen to identify the most promising. While we found that dTPT3-dNaM is generally the most promising UBP, we identified several others that are replicated nearly as well and significantly better than d5SICS-dNaM, and are thus viable candidates for the expansion of the genetic alphabet of a living organism. Moreover, the results suggest that continued optimization should be possible, and that the putatively essential hydrogen-bond acceptor at the position ortho to the glycosidic linkage may not be required. These results clearly demonstrate the generality of hydrophobic forces for the control of base pairing within DNA, provide a wealth of new structure–activity relationship data and importantly identify multiple new candidates for in vivo evaluation and further optimization. PMID:25122747

  13. Pair-bonded humans conform to sexual stereotypes in web-based advertisements for extra-marital partners.

    PubMed

    Kelley, Trish C; Hare, James F

    2010-10-20

    Partners advertisements provide advertisers with access to a large pool of prospective mates, and have proven useful in documenting sex differences in human mating preferences. We coded data from an Internet site (AshleyMadison.com) catering to advertisers engaged in existing pair-bonded relationships. While we predicted that pair-bonding may liberate advertisers from conforming to sexual stereotypes of male promiscuity and female choosiness, our results are uniformly consistent with those stereotypes. Our findings thus provide further evidence that human mating behavior is highly constrained by fundamental biological differences between males and females.

  14. Modeller subjectivity and calibration impacts on hydrological model applications: an event-based comparison for a road-adjacent catchment in south-east Norway.

    PubMed

    Kalantari, Zahra; Lyon, Steve W; Jansson, Per-Erik; Stolte, Jannes; French, Helen K; Folkeson, Lennart; Sassner, Mona

    2015-01-01

    Identifying a 'best' performing hydrologic model in a practical sense is difficult due to the potential influences of modeller subjectivity on, for example, calibration procedure and parameter selection. This is especially true for model applications at the event scale where the prevailing catchment conditions can have a strong impact on apparent model performance and suitability. In this study, two lumped models (CoupModel and HBV) and two physically-based distributed models (LISEM and MIKE SHE) were applied to a small catchment upstream of a road in south-eastern Norway. All models were calibrated to a single event representing typical winter conditions in the region and then applied to various other winter events to investigate the potential impact of calibration period and methodology on model performance. Peak flow and event-based hydrographs were simulated differently by all models leading to differences in apparent model performance under this application. In this case-study, the lumped models appeared to be better suited for hydrological events that differed from the calibration event (i.e., events when runoff was generated from rain on non-frozen soils rather than from rain and snowmelt on frozen soil) while the more physical-based approaches appeared better suited during snowmelt and frozen soil conditions more consistent with the event-specific calibration. This was due to the combination of variations in subsurface conditions over the eight events considered, the subsequent ability of the models to represent the impact of the conditions (particularly when subsurface conditions varied greatly from the calibration event), and the different approaches adopted to calibrate the models. These results indicate that hydrologic models may not only need to be selected on a case-by-case basis but also have their performance evaluated on an application-by-application basis since how a model is applied can be equally important as inherent model structure.

  15. Absorption and fluorescence emission spectroscopic characters of naphtho-homologated yy-DNA bases and effect of methanol solution and base pairing.

    PubMed

    Zhang, Laibin; Li, Huifang; Li, Jilai; Chen, Xiaohua; Bu, Yuxiang

    2010-03-01

    A comprehensive theoretical study of electronic transitions of naphtho-homologated base analogs, namely, yy-T, yy-C, yy-A, and yy-G, was performed. The nature of the low-lying excited states is discussed, and the results are compared with those from experiment and also with those of y-bases. Geometrical characteristics of the lowest excited singlet pipi* and npi* states were explored using the CIS method, and the effects of methanol solution and paring with their complementary natural bases on the relevant absorption and emission spectra of these modified bases were examined. The calculated excitation and emission energies agree well with the measured data, where experimental results are available. In methanol solution, the fluorescence from yy-A and yy-G would be expected to occur around 539 and 562 nm, respectively, suggesting that yy-A is a green-colored fluorophore, whereas yy-G is a yellow-colored fluorophore. The methanol solution was found to red-shift both the absorption and emission maxima of yy-A, yy-T, and yy-C, but blue-shift those for yy-G. Generally, though base pairing has no significant effects on the absorption and fluorescence maxima of yy-A, yy-C, and yy-T, it blue-shifts those for yy-G.

  16. Comparison of SIFT and SURF based DEM extraction approaches on a GEOEYE-1 satellite stereo-pair

    NASA Astrophysics Data System (ADS)

    Daliakopoulos, Ioannis; Tsanis, Ioannis

    2014-05-01

    A MATLAB module for Digital Elevation Model (DEM) extraction from Very High Resolution (VHR) satellite stereo-pair imagery is used to compare the efficiency of two well established feature detection and description algorithms. A procedure for parallel processing of cascading image tiles is used for handling the large datasets requirements of VHR satellite imagery. Scale-Invariant Feature Transform (SIFT) and Speeded Up Robust Features (SURF) algorithms are used to detect potentially tentative feature matches in the members of the stereo-pair. The resulting feature pairs are filtered using the RANdom SAmple Consensus (RANSAC) algorithm by using a variable distance threshold. Finally, tentative feature matches are converted to point cloud ground coordinates for DEM generation. A 0.5 m × 0.5 m Geoeye-1 stereo-pair acquired over an area of 25 km2 in the island of Crete, Greece is used as input for the module. The resulting 2 m × 2 m DEMs has superior detail over previously developed 2 m and 5 m DEMs that are used as reference, and yields a Root Mean Square Error (RMSE) of about 1 m compared to ground truth measurements. Results suggest that SURF's superior runtime performance outweighs the slightly better feature quality attained with SIFT.

  17. Photon-pair source with controllable delay based on shaped inhomogeneous broadening of rare-earth-metal-doped solids

    SciTech Connect

    Sekatski, Pavel; Sangouard, Nicolas; Gisin, Nicolas; Afzelius, Mikael; Riedmatten, Hugues de

    2011-05-15

    Spontaneous Raman emission in atomic gases provides an attractive source of photon pairs with a controllable delay. We show how this technique can be implemented in solid state systems by appropriately shaping the inhomogeneous broadening. Our proposal is eminently feasible with current technology and provides a realistic solution to entangle remote rare-earth-metal-doped solids in a heralded way.

  18. Climatic Factors Drive Population Divergence and Demography: Insights Based on the Phylogeography of a Riparian Plant Species Endemic to the Hengduan Mountains and Adjacent Regions

    PubMed Central

    Wang, Zhi-Wei; Chen, Shao-Tian; Nie, Ze-Long; Zhang, Jian-Wen; Zhou, Zhuo; Deng, Tao; Sun, Hang

    2015-01-01

    Quaternary climatic factors have played a significant role in population divergence and demography. Here we investigated the phylogeography of Osteomeles schwerinae, a dominant riparian plant species of the hot/warm-dry river valleys of the Hengduan Mountains (HDM), Qinling Mountains (QLM) and Yunnan-Guizhou Plateau (YGP). Three chloroplast DNA (cpDNA) regions (trnD-trnT, psbD-trnT, petL-psbE), one single copy nuclear gene (glyceraldehyde 3-phosphate dehydrogenase; G3pdh), and climatic data during the Last Interglacial (LIG; c. 120–140 ka), Last Glacial Maximum (LGM; c. 21 ka), and Current (c. 1950–2000) periods were used in this study. Six cpDNA haplotypes and 15 nuclear DNA (nDNA) haplotypes were identified in the 40 populations of O. schwerinae. Spatial Analysis of Molecular Variance, median-joining networks, and Bayesian phylogenetic trees based on the cpDNA and nDNA datasets, all suggested population divergence between the QLM and HDM-YGP regions. Our climatic analysis identified significant heterogeneity of the climatic factors in the QLM and HDM-YGP regions during the aforementioned three periods. The divergence times based on cpDNA and nDNA haplotypes were estimated to be 466.4–159.4 ka and 315.8–160.3 ka, respectively, which coincide with the time of the weakening of the Asian monsoons in these regions. In addition, unimodal pairwise mismatch distribution curves, expansion times, and Ecological Niche Modeling suggested a history of population expansion (rather than contraction) during the last glaciation. Interestingly, the expansion times were found being well consistent with the intensification of the Asian monsoons during this period. We inferred that the divergence between the two main lineages is probably caused by disruption of more continuous distribution because of weakening of monsoons/less precipitation, whilst subsequent intensification of the Asian monsoons during the last glaciation facilitated the expansion of O. schwerinae

  19. The molecular marker-based comparison of Azotobacter spp. populations isolated from industrial soils of Cracow-Nowa Huta steelworks (southern Poland) and the adjacent agricultural soils.

    PubMed

    Lenart-Boroń, Anna M; Wolny-Koładka, Katarzyna A; Boroń, Piotr M; Mitka, Józef R

    2014-01-01

    The occurrence of Azotobacter spp., which has beneficial effects on plant development, is related to various soil properties, such as pH and fertility. This study evaluated the prevalence of Azotobacter spp. in industrial (H) and agricultural soils (P) in Nowa Huta, Cracow and determined the phenotypic and genetic diversity of these bacteria. The examined bacteria were present in 40% of H and in 50% of P soils. Taxonomic identification of the bacterial isolates indicated the presence of three species--A. salinestris, A. chroococcum and A. vinelandii. The genetic diversity, determined using two fingerprinting methods--Random Analysis of Polymorphic DNA (RAPD) and Rep-PCR (BOX) revealed high level of population diversity. In AMOVA analysis most of diversity was attributed to within-population variation (76-85%), and only 3.78-6.18% was associated with among-group H and P variation. Global test of differences revealed distinct population structure within bacterial strains isolated from H and P areas only for BOX markers (Fst = 0.05732, P = 0.00275). Phenetic analyses: UPGMA and DCA better discriminated H and P groups based on RAPD data. Both BOX and RAPD methods provided an insight into the genetic complexity of Azotobacter spp. variation in soils of different land-use types. PMID:24798904

  20. The molecular marker-based comparison of Azotobacter spp. populations isolated from industrial soils of Cracow-Nowa Huta steelworks (southern Poland) and the adjacent agricultural soils.

    PubMed

    Lenart-Boroń, Anna M; Wolny-Koładka, Katarzyna A; Boroń, Piotr M; Mitka, Józef R

    2014-01-01

    The occurrence of Azotobacter spp., which has beneficial effects on plant development, is related to various soil properties, such as pH and fertility. This study evaluated the prevalence of Azotobacter spp. in industrial (H) and agricultural soils (P) in Nowa Huta, Cracow and determined the phenotypic and genetic diversity of these bacteria. The examined bacteria were present in 40% of H and in 50% of P soils. Taxonomic identification of the bacterial isolates indicated the presence of three species--A. salinestris, A. chroococcum and A. vinelandii. The genetic diversity, determined using two fingerprinting methods--Random Analysis of Polymorphic DNA (RAPD) and Rep-PCR (BOX) revealed high level of population diversity. In AMOVA analysis most of diversity was attributed to within-population variation (76-85%), and only 3.78-6.18% was associated with among-group H and P variation. Global test of differences revealed distinct population structure within bacterial strains isolated from H and P areas only for BOX markers (Fst = 0.05732, P = 0.00275). Phenetic analyses: UPGMA and DCA better discriminated H and P groups based on RAPD data. Both BOX and RAPD methods provided an insight into the genetic complexity of Azotobacter spp. variation in soils of different land-use types.

  1. A nonparametric regression-based linkage scan of rheumatoid factor-IgM using sib-pair squared sums and differences

    PubMed Central

    Ghosh, Saurabh; Rao, P Samba Siva; De, Gourab; Majumder, Partha P

    2007-01-01

    Parametric linkage methods for quantitative trait locus mapping require explicit specification of the probability model of the quantitative trait and hence can lead to misleading linkage inferences when the model assumptions are not valid. Ghosh and Majumder developed a nonparametric regression method based on kernel-smoothing for linkage mapping of quantitative trait locus using squared differences in trait values of independent sib pairs, which is relatively more robust than parametric methods with respect to violations in distributional assumptions. In this study, we modify the above mentioned nonparametric regression method by considering local linear polynomials instead of the Nadaraya-Watson estimator and squared sums of sib-pair trait values in addition to squared differences to perform a genome-wide scan of rheumatoid factor-IgM levels on sib pairs in the Genetic Analysis Workshop 15 simulated data set. We obtain significant evidence of linkage very close to the quantitative trait locus controlling for RF-IgM. We find that the simultaneous use of squared differences and squared sums increases the power to detect linkage compared to using only squared differences. However, because of all the sib pairs are selected for rheumatoid arthritis, there is reduced variance of RF-IgM values, and empirical power to detect linkage is not very high. We also compare the performance of our method with two linear regression approaches: the classical Haseman-Elston method using squared sib-pair trait differences and its extension proposed by Elston et al. using mean-corrected sib-pair cross-products. We find that the proposed nonparametric method yields more power than the linear regression approaches. PMID:18466603

  2. Influence of carboxylic ion-pairing reagents on retention of peptides in thin-layer chromatography systems with C18 silica-based adsorbents.

    PubMed

    Gwarda, Radosław Ł; Aletańska-Kozak, Monika; Klimek-Turek, Anna; Ziajko-Jankowska, Agnieszka; Matosiuk, Dariusz; Dzido, Tadeusz H

    2016-04-01

    One of the main problems related to chromatography of peptides concerns adverse interactions of their strong basic groups with free silanol groups of the silica based stationary phase. Influence of type and concentration of ion-pairing regents on peptide retention in reversed-phase high-performance liquid chromatography (RP-HPLC) systems has been discussed before. Here we present influence of these mobile phase additives on retention of some peptide standards in high-performance thin-layer chromatography (HPTLC) systems with C18 silica-based adsorbents. We prove, that due to different characteristic of adsorbents used in both techniques (RP HPLC and HPTLC), influence of ion-pairing reagents on retention of basic and/or amphoteric compounds also may be quite different. C18 silica-based HPTLC adsorbents provide more complex mechanism of retention and should be rather considered as mixed-mode adsorbents.

  3. In vitro recognition of DNA base pairs by histones in histone-DNA complexes and reconstituted core particles: an ultraviolet resonance Raman study.

    PubMed Central

    Laigle, A; Chinsky, L; Turpin, P Y; Liquier, J; Taillandier, E

    1982-01-01

    Resonance Raman spectra of complexes between DNA and the four core histones, alone or associated, have been investigated in vitro using excitations at 300 and 257 nm, which give complementary informations about the DNA bases. H2A and H2B fractions recognize the G-C base pairs, while H3 and H4 (arginine rich fractions) recognize the A-T base pairs. The associated fractions form complexes with DNA which yield about the same DNA spectral modifications as the DNA-H4 complexes. This reveals the important role of the arginine rich fractions in the core particle formation and confirms the preferential in vitro assembly of nucleosome cores on A-T rich regions of DNA (25). PMID:7155896

  4. Proton Transfer Induced SOMO-to-HOMO Level Switching in One-Electron Oxidized A-T and G-C Base Pairs: A Density Functional Theory Study

    PubMed Central

    2015-01-01

    In the present study, we show that for one-electron oxidized A-T or G-C base pairs the singly occupied molecular orbital (SOMO) is located on A or G and is lower in energy than the doubly occupied highest-occupied molecular orbital (HOMO) localized to the pyrimidines, T or C. This directs second ionizations to the pyrimidine bases resulting in triplet state diradical dications, (A•+-T•+) and (G•+-C•+). On interbase proton transfer, the SOMO and HOMO levels switch and the second oxidation is redirected to G and A. For G-C, the doubly oxidized singlet G(-H)+-C(H+) is more stable than its triplet (G•+-C•+); however, for A-T, the triplet (A•+-T•+) lies lowest in energy. The study demonstrates that double ionization of the A-T base pair results in a triplet dication diradical, which is more stable than the proton-transferred triplet or singlet species; whereas, double ionization of the G-C base pair, the proton transferred doubly oxidized singlet, G(-H)+-C(H+), is more stable and has both oxidations on guanine. In DNA, with both A-T and G-C, multiple oxidations would transfer to the guanine base alone. PMID:24798145

  5. Internucleotide J-couplings and chemical shifts of the N-H···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs.

    PubMed

    Li, Huifang; Zhang, Laibin; Han, Li; Sun, Wenming; Bu, Yuxiang

    2011-04-30

    Internucleotide (2h)J(NN) spin-spin couplings and chemical shifts (δ((1)H) and Δδ((15)N)) of N-H···N H-bond units in the natural and radiation-damaged G-C base pairs were predicted using the appropriate density functional theory calculations with a large basis set. Four possible series of the damaged G-C pairs (viz., dehydrogenated and deprotonated G-C pairs, GC(•-) and GC(•+) radicals) were discussed carefully in this work. Computational NMR results show that radicalization and anionization of the base pairs can yield strong effect on their (2h)J(NN) spin scalar coupling constants and the corresponding chemical shifts. Thus, variations of the NMR parameters associated with the N-H···N H-bonds may be taken as an important criterion for prejudging whether the natural G-C pair is radiation-damaged or not. Analysis shows that (2h)J(NN) couplings are strongly interrelated with the energy gaps (ΔE(LP→σ*)) and the second-order interaction energies (E(2)) between the donor N lone-pair (LP(N)) and the acceptor σ*(N-H) localized NBO orbitals, and also are sensitive to the electron density distributions over the σ*(N-H) orbital, indicating that (2h)J(NN) couplings across the N-H···N H-bonds are charge-transfer-controlled. This is well supported by variation of the electrostatic potential surfaces and corresponding charge transfer amount between G and C moieties. It should be noted that although the NMR spectra for the damaged G-C pair radicals are unavailable now and the states of the radicals are usually detected by the electron spin resonance, this study provides a correlation of the properties of the damaged DNA species with some of the electronic parameters associated with the NMR spectra for the understanding of the different state character of the damaged DNA bases.

  6. Investigation of the Role of the Histidine-Aspartate Pair in the Human Exonuclease III-like Abasic Endonuclease, Ape1

    SciTech Connect

    Lowry, David F. ); Hoyt, David W. ); Khazi, Fayaz A.; Bagu, John R. ); Lindsey, Andrea G.; Wilson, David M.

    2003-05-30

    Hydrogen bonded histidine-aspartate (His-Asp) pairs are critical constituents in several key enzymatic reactions. To date, the role that these pairs play in catalysis is best understood in serine and trypsin-like proteases, where structural and biochemical NMR studies have revealed important pKa values and hydrogen-bonding patterns within the catalytic pocket. However, the role of the His-Asp pair in metal-assisted catalysis is less clear. Here, we apply liquid state NMR to investigate the role of a critical histidine of apurinic endonuclease 1 (Ape1), a human DNA repair enzyme that cleaves adjacent to abasic sites in DNA using one or more divalent cations and an active site His-Asp pair. The studies within suggest that the Ape1 His- Asp pair functions as neither a general base catalyst nor a metal ligand. Rather, the pair likely stabilizes the pentavalent transition state necessary for phospho-transfer.

  7. A homonuclear spin-pair filter for solid-state NMR based on adiabatic-passage techniques

    NASA Astrophysics Data System (ADS)

    Verel, René; Baldus, Marc; Ernst, Matthias; Meier, Beat H.

    1998-05-01

    A filtering scheme for the selection of spin pairs (and larger spin clusters) under fast magic-angle spinning is proposed. The scheme exploits the avoided level crossing in spin pairs during an adiabatic amplitude sweep through the so-called HORROR recoupling condition. The advantages over presently used double-quantum filters are twofold. (i) The maximum theoretical filter efficiency is, due to the adiabatic variation, 100% instead of 73% as for transient methods. (ii) Since the filter does not rely on the phase-cycling properties of the double-quantum coherence, there is no need to obtain the full double-quantum intensity for all spins in the sample at one single point in time. The only important requirement is that all coupled spins pass through a two-spin state during the amplitude sweep. This makes the pulse scheme robust with respect to rf-amplitude missetting, rf-field inhomogeneity and chemical-shift offset.

  8. Historical Matching Strategies in Kidney Paired Donation: The 7-Year Evolution of a Web-Based Virtual Matching System.

    PubMed

    Fumo, D E; Kapoor, V; Reece, L J; Stepkowski, S M; Kopke, J E; Rees, S E; Smith, C; Roth, A E; Leichtman, A B; Rees, M A

    2015-10-01

    Failure to convert computer-identified possible kidney paired donation (KPD) exchanges into transplants has prohibited KPD from reaching its full potential. This study analyzes the progress of exchanges in moving from "offers" to completed transplants. Offers were divided into individual segments called 1-way transplants in order to calculate success rates. From 2007 to 2014, the Alliance for Paired Donation performed 243 transplants, 31 in collaboration with other KPD registries and 194 independently. Sixty-one of 194 independent transplants (31.4%) occurred via cycles, while the remaining 133 (68.6%) resulted from nonsimultaneous extended altruistic donor (NEAD) chains. Thirteen of 35 (37.1%) NEAD chains with at least three NEAD segments accounted for 68% of chain transplants (8.6 tx/chain). The "offer" and 1-way success rates were 21.9 and 15.5%, respectively. Three reasons for failure were found that could be prospectively prevented by changes in protocol or software: positive laboratory crossmatch (28%), transplant center declined donor (17%) and pair transplanted outside APD (14%). Performing a root cause analysis on failures in moving from offer to transplant has allowed the APD to improve protocols and software. These changes have improved the success rate and the number of transplants performed per year.

  9. A 53-base-pair inverted repeat negatively regulates expression of the adjacent and divergently oriented cytochrome P450(BM-1) gene and its regulatory gene, bm1P1, in Bacillus megaterium.

    PubMed Central

    Shaw, G C; Sung, C C; Liu, C H; Kao, H S

    1997-01-01

    To study the role of the cis-acting element(s) in controlling the expression of the cytochrome P450(BM-1) gene and its upstream regulatory gene, bm1P1, in Bacillus megaterium, various deletion derivatives were constructed. A 53-bp inverted repeat located midway between the P450(BM-1) gene and bm1P1 gene was found in vivo to negatively regulate the expression of both genes, the regulation of which may occur at the transcriptional level. The promoter of the P450(BM-1), gene was also identified and found to be similar to those recognized by the sigmaA RNA polymerase of Bacillus subtilis. Possible mechanisms by which the 53-bp inverted repeat regulates the gene expression are discussed. PMID:8982010

  10. Two male adults with pathogenic AUTS2 variants, including a two-base pair deletion, further delineate the AUTS2 syndrome

    PubMed Central

    Beunders, Gea; de Munnik, Sonja A; Van der Aa, Nathalie; Ceulemans, Berten; Voorhoeve, Els; Groffen, Alexander J; Nillesen, Willy M; Meijers-Heijboer, Elizabeth J; Frank Kooy, R; Yntema, Helger G; Sistermans, Erik A

    2015-01-01

    AUTS2 syndrome is characterized by low birth weight, feeding difficulties, intellectual disability, microcephaly and mild dysmorphic features. All affected individuals thus far were caused by chromosomal rearrangements, variants at the base pair level disrupting AUTS2 have not yet been described. Here we present the full clinical description of two affected men with intragenic AUTS2 variants (one two-base pair deletion in exon 7 and one deletion of exon 6). Both variants are de novo and are predicted to cause a frameshift of the full-length transcript but are unlikely to affect the shorter 3′ transcript starting in exon 9. The similarities between the phenotypes of both men are striking and further support that AUTS2 syndrome is a single gene disorder. PMID:25205402

  11. A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs.

    PubMed

    Marchetti, Barbara; Karsili, Tolga N V; Ashfold, Michael N R; Domcke, Wolfgang

    2016-07-27

    The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs. PMID:26980149

  12. A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs.

    PubMed

    Marchetti, Barbara; Karsili, Tolga N V; Ashfold, Michael N R; Domcke, Wolfgang

    2016-07-27

    The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.

  13. Architecture based on the integration of intermolecular G-quadruplex structure with sticky-end pairing and colorimetric detection of DNA hybridization

    NASA Astrophysics Data System (ADS)

    Li, Hongbo; Wu, Zai-Sheng; Shen, Zhifa; Shen, Guoli; Yu, Ruqin

    2014-01-01

    An interesting discovery is reported in that G-rich hairpin-based recognition probes can self-assemble into a nano-architecture based on the integration of an intermolecular G-quadruplex structure with the sticky-end pairing effect in the presence of target DNAs. Moreover, GNPs modified with partly complementary DNAs can intensively aggregate by hybridization-based intercalation between intermolecular G-quadruplexes, indicating an inspiring assembly mechanism and a powerful colorimetric DNA detection. The proposed intermolecular G-quadruplex-integrated sticky-end pairing assembly (called GISA)-based colorimetric system allows a specific and quantitative assay of p53 DNA with a linear range of more than two orders of magnitude and a detection limit of 0.2 nM, suggesting a considerably improved analytical performance. And more to the point, the discrimination of single-base mismatched target DNAs can be easily conducted via visual observation. The successful development of the present colorimetric system, especially the GISA-based aggregation mechanism of GNPs is different from traditional approaches, and offers a critical insight into the dependence of the GNP aggregation on the structural properties of oligonucleotides, opening a good way to design colorimetric sensing probes and DNA nanostructure. An interesting discovery is reported in that G-rich hairpin-based recognition probes can self-assemble into a nano-architecture based on the integration of an intermolecular G-quadruplex structure with the sticky-end pairing effect in the presence of target DNAs. Moreover, GNPs modified with partly complementary DNAs can intensively aggregate by hybridization-based intercalation between intermolecular G-quadruplexes, indicating an inspiring assembly mechanism and a powerful colorimetric DNA detection. The proposed intermolecular G-quadruplex-integrated sticky-end pairing assembly (called GISA)-based colorimetric system allows a specific and quantitative assay of p53 DNA

  14. The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine-cytosine base pairs in Watson-Crick and Hoogsteen configurations.

    PubMed

    Bende, Attila; Muntean, Cristina M

    2014-03-01

    The theoretical IR and Raman spectra of the guanine-cytosine DNA base pairs in Watson-Crick and Hoogsteen configurations were computed using DFT method with M06-2X meta-hybrid GGA exchange-correlation functional, including the anharmonic corrections and solvent effects. The results for harmonic frequencies and their anharmonic corrections were compared with our previously calculated values obtained with the B3PW91 hybrid GGA functional. Significant differences were obtained for the anharmonic corrections calculated with the two different DFT functionals, especially for the stretching modes, while the corresponding harmonic frequencies did not differ considerable. For the Hoogtseen case the H⁺ vibration between the G-C base pair can be characterized as an asymmetric Duffing oscillator and therefore unrealistic anharmonic corrections for normal modes where this proton vibration is involved have been obtained. The spectral modification due to the anharmonic corrections, solvent effects and the influence of sugar-phosphate group for the Watson-Crick and Hoogsteen base pair configurations, respectively, were also discussed. For the Watson-Crick case also the influence of the stacking interaction on the theoretical IR and Raman spectra was analyzed. Including the anharmonic correction in our normal mode analysis is essential if one wants to obtain correct assignments of the theoretical frequency values as compared with the experimental spectra. PMID:24567152

  15. Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.

    PubMed

    Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Šebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovský, Vladimír; Kojima, Chojiro; Tanaka, Yoshiyuki

    2016-09-01

    The structure of an Ag(I) -mediated cytosine-cytosine base pair, C-Ag(I) -C, was determined with NMR spectroscopy in solution. The observation of 1-bond (15) N-(109) Ag J-coupling ((1) J((15) N,(109) Ag): 83 and 84 Hz) recorded within the C-Ag(I) -C base pair evidenced the N3-Ag(I) -N3 linkage in C-Ag(I) -C. The triplet resonances of the N4 atoms in C-Ag(I) -C demonstrated that each exocyclic N4 atom exists as an amino group (-NH2 ), and any isomerization and/or N4-Ag(I) bonding can be excluded. The 3D structure of Ag(I) -DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C-Ag(I) -C (-18.3±3.0°). The (109) Ag NMR chemical shift of C-Ag(I) -C was recorded for cytidine/Ag(I) complex (δ((109) Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C-Ag(I) -C base pair. PMID:27505707

  16. Triple helices formed at oligopyrimidine*oligopurine sequences with base pair inversions: effect of a triplex-specific ligand on stability and selectivity.

    PubMed Central

    Kukreti, S; Sun, J S; Loakes, D; Brown, D M; Nguyen, C H; Bisagni, E; Garestier, T; Helene, C

    1998-01-01

    Oligonucleotide-directed triple helix formation is mostly restricted to oligopyrimidine*oligopurine sequences of double helical DNA. An interruption of one or two pyrimidines in the oligopurine target strand leads to a strong triplex destabilisation. We have investigated the effect of nucleotide analogues introduced in the third strand at the site opposite the base pair inversion(s). We show that a 3-nitropyrrole derivative (M) discriminates G*C from C*G, A*T and T*A in the presence of a triplex-specific ligand (a benzo[e]pyridoindole derivative, BePI). N6-methoxy-2,6-diaminopurine (K) binds to an A*T base pair better than a T*A, G*C or C*G base pair. Some discrimination is still observed in the presence of BePI and triplex stability is markedly increased. These findings should help in designing BePI-oligonucleotide conjugates to extend the range of DNA sequences available for triplex formation. PMID:9547278

  17. Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea

    PubMed Central

    Tian, Lei; Zhang, Zhenfeng; Wang, Hanqian; Zhao, Mohan; Dong, Yuhui; Gong, Yong

    2016-01-01

    T:G base pair arising from spontaneous deamination of 5mC or polymerase errors is a great challenge for DNA repair of hyperthermophilic archaea, especially Crenarchaea. Most strains in this phylum lack the protein homologues responsible for the recognition of the mismatch in the DNA repair pathways. To investigate whether Cren7, a highly conserved chromatin protein in Crenarchaea, serves a role in the repair of T:G mispairs, the crystal structures of Cren7-GTAATTGC and Cren7-GTGATCGC complexes were solved at 2.0 Å and 2.1 Å. In our structures, binding of Cren7 to the AT-rich DNA duplex (GTAATTGC) induces opening of T2:G15 but not T10:G7 base pair. By contrast, both T:G mispairs in the GC-rich DNA duplex (GTGATCGC) retain the classic wobble type. Structural analysis also showed DNA helical changes of GTAATTGC, especially in the steps around the open T:G base pair, as compared to GTGATCGC or the matched DNAs. Surface plasmon resonance assays revealed a 4-fold lower binding affinity of Cren7 for GTAATTGC than that for GTGATCGC, which was dominantly contributed by the decrease of association rate. These results suggested that binding of Cren7 to DNA leads to T:G mispair opening in a sequence dependent manner, and therefore propose the potential roles of Cren7 in DNA repair. PMID:27685992

  18. Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.

    PubMed

    Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Šebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovský, Vladimír; Kojima, Chojiro; Tanaka, Yoshiyuki

    2016-09-01

    The structure of an Ag(I) -mediated cytosine-cytosine base pair, C-Ag(I) -C, was determined with NMR spectroscopy in solution. The observation of 1-bond (15) N-(109) Ag J-coupling ((1) J((15) N,(109) Ag): 83 and 84 Hz) recorded within the C-Ag(I) -C base pair evidenced the N3-Ag(I) -N3 linkage in C-Ag(I) -C. The triplet resonances of the N4 atoms in C-Ag(I) -C demonstrated that each exocyclic N4 atom exists as an amino group (-NH2 ), and any isomerization and/or N4-Ag(I) bonding can be excluded. The 3D structure of Ag(I) -DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C-Ag(I) -C (-18.3±3.0°). The (109) Ag NMR chemical shift of C-Ag(I) -C was recorded for cytidine/Ag(I) complex (δ((109) Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C-Ag(I) -C base pair.

  19. Combined Monte Carlo and quantum mechanics study of the hydration of the guanine-cytosine base pair.

    PubMed

    Coutinho, Kaline; Ludwig, Valdemir; Canuto, Sylvio

    2004-06-01

    We present a computer simulation study of the hydration of the guanine-cytosine (GC) hydrogen-bonded complex. Using first principles density-functional theory, with gradient-corrected exchange-correlation and Monte Carlo simulation, we include thermal contribution, structural effects, solvent polarization, and the water-water and water-GC hydrogen bond interaction to show that the GC interaction in an aqueous environment is weakened to about 70% of the value obtained for an isolated complex. We also analyze in detail the preferred hydration sites of the GC pair and show that on the average it makes around five hydrogen bonds with water.

  20. Large anomalous-dispersion mode-locked fiber laser based on a chirped fiber Bragg grating pair

    NASA Astrophysics Data System (ADS)

    Wang, Jie; Yan, Yaxi; Hu, Chengzhi; Wu, Bo; Shen, Yonghang

    2016-10-01

    A carbon-nanotube mode-locked erbium fiber laser with large net anomalous dispersion is presented. A chirped fiber Bragg grating (CFBG) pair is incorporated to increase the net-cavity anomalous dispersion and soliton splitting threshold. Self-started mode-locked laser produces stable pulses with repetition rate of 9.26 MHz. Laser spectrum is centered at ~1560 nm with 3 dB bandwidth of 0.43 nm. The typical output pulse energy and duration is 0.21 nJ and 8.05 ps, respectively.

  1. Analysis of adjacent segment reoperation after lumbar total disc replacement

    PubMed Central

    Rainey, Scott; Blumenthal, Scott L.; Zigler, Jack E.; Guyer, Richard D.; Ohnmeiss, Donna D.

    2012-01-01

    Background Fusion has long been used for treating chronic back pain unresponsive to nonoperative care. However, potential development of adjacent segment degeneration resulting in reoperation is a concern. Total disc replacement (TDR) has been proposed as a method for addressing back pain and preventing or reducing adjacent segment degeneration. The purpose of the study was to determine the reoperation rate at the segment adjacent to a level implanted with a lumbar TDR and to analyze the pre-TDR condition of the adjacent segment. Methods This study was based on a retrospective review of charts and radiographs from a consecutive series of 1000 TDR patients to identify those who underwent reoperation because of adjacent segment degeneration. Some of the patients were part of randomized studies comparing TDR with fusion. Adjacent segment reoperation data were also collected from 67 patients who were randomized to fusion in those studies. The condition of the adjacent segment before the index surgery was compared with its condition before reoperation based on radiographs, magnetic resonance imaging (MRI), and computed tomography. Results Of the 1000 TDR patients, 20 (2.0%) underwent reoperation. The mean length of time from arthroplasty to reoperation was 28.3 months (range, 0.5–85 months). Of the adjacent segments evaluated on preoperative MRI, 38.8% were normal, 38.8% were moderately diseased, and 22.2% were classified as having severe degeneration. None of these levels had a different grading at the time of reoperation compared with the pre-TDR MRI study. Reoperation for adjacent segment degeneration was performed in 4.5% of the fusion patients. Conclusions The 2.0% rate of adjacent segment degeneration resulting in reoperation in this study is similar to the 2.0% to 2.8% range in other studies and lower than the published rates of 7% to 18% after lumbar fusion. By carefully assessing the presence of pre-existing degenerative changes before performing arthroplasty

  2. 1. OVERVIEW SHOWING FIRING CONTROL BLOCKHOUSE 0502 AND ADJACENT OBSERVATION ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. OVERVIEW SHOWING FIRING CONTROL BLOCKHOUSE 0502 AND ADJACENT OBSERVATION TOWER. WATER BRAKE TROUGH SEGMENT AT LOWER RIGHT. Looking north northeast. - Edwards Air Force Base, South Base Sled Track, Firing & Control Blockhouse for 10,000-foot Track, South of Sled Track at midpoint of 20,000-foot track, Lancaster, Los Angeles County, CA

  3. Merging Problem-Based Learning with Simulation-Based Learning in the Medical Undergraduate Curriculum: The PAIRED Framework for Enhancing Lifelong Learning

    PubMed Central

    Koh, Jansen

    2016-01-01

    Lifelong learning is an essential trait that is expected of every physician. The CanMeds 2005 Physician Competency Framework emphasizes lifelong learning as a key competency that physicians must achieve in becoming better physicians. However, many physicians are not competent at engaging in lifelong learning. The current medical education system is deficient in preparing medical students to develop and carry out their own lifelong learning curriculum upon graduation. Despite understanding how physicians learn at work, medical students are not trained to learn while working. Similarly, although barriers to lifelong learning are known, medical students are not adequately skilled in overcoming these barriers. Learning to learn is just as important, if not more, as acquiring the skills and knowledge required of a physician. The medical undergraduate curriculum lacks a specific learning strategy to prepare medical students in becoming an adept lifelong learner. In this article, we propose a learning strategy for lifelong learning at the undergraduate level. In developing this novel strategy, we paid particular attention to two parameters. First, this strategy should be grounded on literature describing a physician’s lifelong learning process. Second, the framework for implementing this strategy must be based on existing undergraduate learning strategies to obviate the need for additional resources, learner burden, and faculty time. In this paper, we propose a Problem, Analysis, Independent Research Reporting, Experimentation Debriefing (PAIRED) framework that follows the learning process of a physician and serves to synergize the components of problem-based learning and simulation-based learning in specifically targeting the barriers to lifelong learning. PMID:27446767

  4. Anomalous scaling of Δ C versus T c in the Fe-based superconductors: the $${S}_{\\pm }$$-wave pairing state model

    DOE PAGES

    Bang, Yunkyu; Stewart, G. R.

    2016-02-01

    The strong power law behavior of the specific heat jumpmore » $${\\rm{\\Delta }}C\\;$$ versus T c $$({\\rm{\\Delta }}C/{T}_{{\\rm{c}}}\\sim {T}_{{\\rm{c}}}^{\\alpha },\\alpha \\approx 2)$$, first observed by Bud'ko et al (2009 Phys. Rev. B 79 220516), has been confirmed with several families of the Fe-based superconducting compounds with various dopings. We tested a minimal two band BCS model to understand this anomalous behavior and showed that this non-BCS relation between $${\\rm{\\Delta }}C\\;$$ versus T c is a generic property of the multiband superconducting state paired by a dominant interband interaction ($${V}_{\\mathrm{inter}}\\gt {V}_{\\mathrm{intra}}$$) reflecting the relation $$\\frac{{{\\rm{\\Delta }}}_{{\\rm{h}}}}{{{\\rm{\\Delta }}}_{{\\rm{e}}}}\\sim \\sqrt{\\frac{{N}_{{\\rm{e}}}}{{N}_{{\\rm{h}}}}}$$ near T c, as in the $${S}_{\\pm }$$-wave pairing state. We also found that this $${\\rm{\\Delta }}C\\;$$ versus T c power law can continuously change from the ideal BNC scaling to a considerable deviation by a moderate variation of the impurity scattering rate $${{\\rm{\\Gamma }}}_{0}$$ (non-pair-breaking). Finally, as a result, our model provides a consistent explanation why the electron-doped Fe-based superconductors follow the ideal BNC scaling very well while the hole-doped systems often show varying degree of deviations.« less

  5. Anomalous scaling of ΔC versus T c in the Fe-based superconductors: the {S}_{+/- }-wave pairing state model

    NASA Astrophysics Data System (ADS)

    Bang, Yunkyu; Stewart, G. R.

    2016-02-01

    The strong power law behavior of the specific heat jump {{Δ }}C versus T c ({{Δ }}C/{T}{{c}}∼ {T}{{c}}α ,α ≈ 2), first observed by Bud’ko et al (2009 Phys. Rev. B 79 220516), has been confirmed with several families of the Fe-based superconducting compounds with various dopings. We have tested a minimal two band BCS model to understand this anomalous behavior and showed that this non-BCS relation between {{Δ }}C versus T c is a generic property of the multiband superconducting state paired by a dominant interband interaction ({V}{inter}\\gt {V}{intra}) reflecting the relation \\frac{{{{Δ }}}{{h}}}{{{{Δ }}}{{e}}}∼ \\sqrt{\\frac{{N}{{e}}}{{N}{{h}}}} near T c, as in the {S}+/- -wave pairing state. We also found that this {{Δ }}C versus T c power law can continuously change from the ideal BNC scaling to a considerable deviation by a moderate variation of the impurity scattering rate {{{Γ }}}0 (non-pair-breaking). As a result, our model provides a consistent explanation why the electron-doped Fe-based superconductors follow the ideal BNC scaling very well while the hole-doped systems often show varying degree of deviations.

  6. A tilt-pair based method for assigning the projection directions of randomly oriented single-particle molecules.

    PubMed

    Ueno, Yutaka; Mine, Shouhei; Kawasaki, Kazunori

    2015-04-01

    In this article, we describe an improved method to assign the projection angle for averaged images using tilt-pair images for three-dimensional reconstructions from randomly oriented single-particle molecular images. Our study addressed the so-called 'initial volume problem' in the single-particle reconstruction, which involves estimation of projection angles of the particle images. The projected images of the particles in different tilt observations were mixed and averaged for the characteristic views. After the ranking of these group average images in terms of reliable tilt angle information, mutual tilt angles between images are assigned from the constituent tilt-pair information. Then, multiples of the conical tilt series are made and merged to construct a network graph of the particle images in terms of projection angles, which are optimized for the three-dimensional reconstruction. We developed the method with images of a synthetic object and applied it to a single-particle image data set of the purified deacetylase from archaea. With the introduction of low-angle tilt observations to minimize unfavorable imaging conditions due to tilting, the results demonstrated reasonable reconstruction models without imposing symmetry to the structure. This method also guides its users to discriminate particle images of different conformational state of the molecule.

  7. Dislocation network with pair-coupling structure in {111} γ/γ' interface of Ni-based single crystal superalloy.

    PubMed

    Ru, Yi; Li, Shusuo; Zhou, Jian; Pei, Yanling; Wang, Hui; Gong, Shengkai; Xu, Huibin

    2016-01-01

    The γ/γ' interface dislocation network is reported to improve the high temperature creep resistance of single crystal superalloys and is usually found to deposit in {001} interface. In this work, a new type of dislocation network was found in {111} γ/γ' interface at a single crystal model superalloy crept at 1100 °C/100 MPa. The dislocations in the network are screw with Burgers vectors of 1/2 a<110> and most interestingly, they exhibit a pair-coupling structure. Further investigation indicates that the formation of {111} interface dislocation network occurs when the γ' raft structure begins to degrade by the dislocations cutting into the rafted γ' through the interface. In this condition, the pair-coupling structure is established by the dislocations gliding in a single {111} plane of γ', in order to remove the anti-phase boundary in γ'; these dislocations also act as diffusion channels for dissolving of the γ' particle that is unstable under the interfacial stress from lattice misfit, which leads to the formation of {111}-type zigzag interface. The formation of this network arises as a consequence of more negative misfit, low-alloying γ' particle and proper test conditions of temperature and stress. PMID:27511822

  8. Dislocation network with pair-coupling structure in {111} γ/γ' interface of Ni-based single crystal superalloy.

    PubMed

    Ru, Yi; Li, Shusuo; Zhou, Jian; Pei, Yanling; Wang, Hui; Gong, Shengkai; Xu, Huibin

    2016-08-11

    The γ/γ' interface dislocation network is reported to improve the high temperature creep resistance of single crystal superalloys and is usually found to deposit in {001} interface. In this work, a new type of dislocation network was found in {111} γ/γ' interface at a single crystal model superalloy crept at 1100 °C/100 MPa. The dislocations in the network are screw with Burgers vectors of 1/2 a<110> and most interestingly, they exhibit a pair-coupling structure. Further investigation indicates that the formation of {111} interface dislocation network occurs when the γ' raft structure begins to degrade by the dislocations cutting into the rafted γ' through the interface. In this condition, the pair-coupling structure is established by the dislocations gliding in a single {111} plane of γ', in order to remove the anti-phase boundary in γ'; these dislocations also act as diffusion channels for dissolving of the γ' particle that is unstable under the interfacial stress from lattice misfit, which leads to the formation of {111}-type zigzag interface. The formation of this network arises as a consequence of more negative misfit, low-alloying γ' particle and proper test conditions of temperature and stress.

  9. Fiber-based photon-pair source capable of hybrid entanglement in frequency and transverse mode, controllably scalable to higher dimensions

    PubMed Central

    Cruz-Delgado, D.; Ramirez-Alarcon, R.; Ortiz-Ricardo, E.; Monroy-Ruz, J.; Dominguez-Serna, F.; Cruz-Ramirez, H.; Garay-Palmett, K.; U’Ren, A. B.

    2016-01-01

    We have designed and implemented a photon-pair source, based on the spontaneous four wave mixing (SFWM) process in a few-mode fiber, in a geometry which permits multiple, simultaneous SFWM processes, each associated with a distinct combination of transverse modes for the four participating waves. In our source: i) each process is group-velocity-matched so that it is, by design, nearly-factorable, and ii) the spectral separation between neighboring processes is greater than the marginal spectral width of each process. Consequently, there is a direct correspondence between the joint amplitude of each process and each of the Schmidt mode pairs of the overall two-photon state. Our approach permits hybrid entanglement in discrete frequency and in transverse mode, whereby control of the number of supported fiber transverse modes allows scalability to higher dimensions while spectral filtering may be used for straightforward Schmidt mode discrimination. PMID:27271284

  10. Fiber-based photon-pair source capable of hybrid entanglement in frequency and transverse mode, controllably scalable to higher dimensions.

    PubMed

    Cruz-Delgado, D; Ramirez-Alarcon, R; Ortiz-Ricardo, E; Monroy-Ruz, J; Dominguez-Serna, F; Cruz-Ramirez, H; Garay-Palmett, K; U'Ren, A B

    2016-01-01

    We have designed and implemented a photon-pair source, based on the spontaneous four wave mixing (SFWM) process in a few-mode fiber, in a geometry which permits multiple, simultaneous SFWM processes, each associated with a distinct combination of transverse modes for the four participating waves. In our source: i) each process is group-velocity-matched so that it is, by design, nearly-factorable, and ii) the spectral separation between neighboring processes is greater than the marginal spectral width of each process. Consequently, there is a direct correspondence between the joint amplitude of each process and each of the Schmidt mode pairs of the overall two-photon state. Our approach permits hybrid entanglement in discrete frequency and in transverse mode, whereby control of the number of supported fiber transverse modes allows scalability to higher dimensions while spectral filtering may be used for straightforward Schmidt mode discrimination. PMID:27271284

  11. Fiber-based photon-pair source capable of hybrid entanglement in frequency and transverse mode, controllably scalable to higher dimensions.

    PubMed

    Cruz-Delgado, D; Ramirez-Alarcon, R; Ortiz-Ricardo, E; Monroy-Ruz, J; Dominguez-Serna, F; Cruz-Ramirez, H; Garay-Palmett, K; U'Ren, A B

    2016-06-07

    We have designed and implemented a photon-pair source, based on the spontaneous four wave mixing (SFWM) process in a few-mode fiber, in a geometry which permits multiple, simultaneous SFWM processes, each associated with a distinct combination of transverse modes for the four participating waves. In our source: i) each process is group-velocity-matched so that it is, by design, nearly-factorable, and ii) the spectral separation between neighboring processes is greater than the marginal spectral width of each process. Consequently, there is a direct correspondence between the joint amplitude of each process and each of the Schmidt mode pairs of the overall two-photon state. Our approach permits hybrid entanglement in discrete frequency and in transverse mode, whereby control of the number of supported fiber transverse modes allows scalability to higher dimensions while spectral filtering may be used for straightforward Schmidt mode discrimination.

  12. Developmentally regulated excision of a 28-base-pair sequence from the Paramecium genome requires flanking DNA.

    PubMed

    Ku, M; Mayer, K; Forney, J D

    2000-11-01

    The micronuclear DNA of Paramecium tetraurelia is estimated to contain over 50,000 short DNA elements that are precisely removed during the formation of the transcriptionally active macronucleus. Each internal eliminated sequence (IES) is bounded by 5'-TA-3' dinucleotide repeats, a feature common to some classes of DNA transposons. We have developed an in vivo assay to analyze these highly efficient and precise DNA excision events. The microinjection of a cloned IES into mating cells results in accurately spliced products, and the transformed cells maintain the injected DNA as extrachromosomal molecules. A series of deletions flanking one side of a 28-bp IES were constructed and analyzed with the in vivo assay. Whereas 72 bp of DNA flanking the eliminated region is sufficient for excision, lengths of 31 and 18 bp result in reduced excision and removal of all wild-type sequences adjacent to the TA results in complete failure of excision. In contrast, nucleotide mutations within the middle of the 28-bp IES do not prevent excision. The results are consistent with a functional role for perfect inverted repeats flanking the IES. PMID:11046136

  13. Pair-Wise, Deformable Mirror, Image Plane-Based Diversity Electric Field Estimation for High Contrast Coronagraphy

    NASA Technical Reports Server (NTRS)

    Give'on, Amir; Kern, Brian D.; Shaklan, Stuart

    2011-01-01

    In this paper we describe the complex electric field reconstruction from image plane intensity measurements for high contrast coronagraphic imaging. A deformable mirror (DM) surface is modied with pairs of complementary shapes to create diversity in the image plane of the science camera where the intensity of the light is measured. Along with the Electric Field Conjugation correction algorithm, this estimation method has been used in various high contrast imaging testbeds to achieve the best contrasts to date both in narrow and in broad band light. We present the basic methodology of estimation in easy to follow list of steps, present results from HCIT and raise several open quations we are confronted with using this method.

  14. A pair of novel Cd(II) enantiomers based on lactate derivatives: Synthesis, crystal structures and properties

    NASA Astrophysics Data System (ADS)

    Xu, Zhong-Xuan; Ao, Ke-Hou; Zhang, Jian

    2016-09-01

    A pair of novel 3D homochiral metal-organic frameworks (HMOFs), namely [Cd2.5((R)-CIA)6(1,4-DIB)(H2O)2]·((CH3)2NH2)·H2O (1-D), [Cd2.5((S)-CIA)6(1,4-DIB)(H2O)2]·((CH3)2NH2)·H2O (1-L), have been synthesized using lactic acid derivative ligands ((R)-H3CIA and (S)-H3CIA) and 1,4-DIB. Crystallographic analyses indicate that the complexes 1-D and 1-L are packed by cage substructures. Some physical characteristics, such as solid-state circular dichroism (CD), thermal stabilities and photoluminescent properties are also investigated. Our results highlight the effective method to apply lactic acid derivative ligands to form interesting HMOFs.

  15. New Theoretical Insight into the Interactions and Properties of Formic Acid: Development of a Quantum-Based Pair Potential for Formic Acid.

    SciTech Connect

    Roszak, S; Gee, R; Balasubramanian, K; Fried, L

    2005-08-08

    We performed ab initio quantum chemical studies for the development of intra and intermolecular interaction potentials for formic acid for use in molecular dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter-molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment.

  16. New theoretical insight into the interactions and properties of formic acid: development of a quantum-based pair potential for formic acid.

    PubMed

    Roszak, Szczepan; Gee, Richard H; Balasubramanian, Krishnan; Fried, Laurence E

    2005-10-01

    We performed ab initio quantum-chemical studies for the development of intra- and intermolecular interaction potentials for formic acid for use in molecular-dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen-bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular-dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular-dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment. PMID:16238411

  17. Key Roles of Lewis Acid-Base Pairs on ZnxZryOz in Direct Ethanol/Acetone to Isobutene Conversion.

    PubMed

    Sun, Junming; Baylon, Rebecca A L; Liu, Changjun; Mei, Donghai; Martin, Kevin J; Venkitasubramanian, Padmesh; Wang, Yong

    2016-01-20

    The effects of surface acidity on the cascade ethanol-to-isobutene conversion were studied using ZnxZryOz catalysts. The ethanol-to-isobutene reaction was found to be limited by the secondary reaction of the key intermediate, acetone, namely the acetone-to-isobutene reaction. Although the catalysts with coexisting Brønsted acidity could catalyze the rate-limiting acetone-to-isobutene reaction, the presence of Brønsted acidity is also detrimental. First, secondary isobutene isomerization is favored, producing a mixture of butene isomers. Second, undesired polymerization and coke formation prevail, leading to rapid catalyst deactivation. Most importantly, both steady-state and kinetic reaction studies as well as FTIR analysis of adsorbed acetone-d6 and D2O unambiguously showed that a highly active and selective nature of balanced Lewis acid-base pairs was masked by the coexisting Brønsted acidity in the aldolization and self-deoxygenation of acetone to isobutene. As a result, ZnxZryOz catalysts with only Lewis acid-base pairs were discovered, on which nearly a theoretical selectivity to isobutene (∼ 88.9%) was successfully achieved, which has never been reported before. Moreover, the absence of Brønsted acidity in such ZnxZryOz catalysts also eliminates the side isobutene isomerization and undesired polymerization/coke reactions, resulting in the production of high purity isobutene with significantly improved catalyst stability (<2% activity loss after 200 h time-on-stream). This work not only demonstrates a balanced Lewis acid-base pair for the highly active and selective cascade ethanol-to-isobutene reaction but also sheds light on the rational design of selective and robust acid-base catalyst for C-C coupling via aldolization reaction. PMID:26624526

  18. Key Roles of Lewis Acid-Base Pairs on ZnxZryOz in Direct Ethanol/Acetone to Isobutene Conversion.

    PubMed

    Sun, Junming; Baylon, Rebecca A L; Liu, Changjun; Mei, Donghai; Martin, Kevin J; Venkitasubramanian, Padmesh; Wang, Yong

    2016-01-20

    The effects of surface acidity on the cascade ethanol-to-isobutene conversion were studied using ZnxZryOz catalysts. The ethanol-to-isobutene reaction was found to be limited by the secondary reaction of the key intermediate, acetone, namely the acetone-to-isobutene reaction. Although the catalysts with coexisting Brønsted acidity could catalyze the rate-limiting acetone-to-isobutene reaction, the presence of Brønsted acidity is also detrimental. First, secondary isobutene isomerization is favored, producing a mixture of butene isomers. Second, undesired polymerization and coke formation prevail, leading to rapid catalyst deactivation. Most importantly, both steady-state and kinetic reaction studies as well as FTIR analysis of adsorbed acetone-d6 and D2O unambiguously showed that a highly active and selective nature of balanced Lewis acid-base pairs was masked by the coexisting Brønsted acidity in the aldolization and self-deoxygenation of acetone to isobutene. As a result, ZnxZryOz catalysts with only Lewis acid-base pairs were discovered, on which nearly a theoretical selectivity to isobutene (∼ 88.9%) was successfully achieved, which has never been reported before. Moreover, the absence of Brønsted acidity in such ZnxZryOz catalysts also eliminates the side isobutene isomerization and undesired polymerization/coke reactions, resulting in the production of high purity isobutene with significantly improved catalyst stability (<2% activity loss after 200 h time-on-stream). This work not only demonstrates a balanced Lewis acid-base pair for the highly active and selective cascade ethanol-to-isobutene reaction but also sheds light on the rational design of selective and robust acid-base catalyst for C-C coupling via aldolization reaction.

  19. A 300 MHz and 600 MHz proton NMR study of a 12 base pair restriction fragment: investigation of structure by relaxation measurements.

    PubMed Central

    Early, T A; Kearns, D R; Hillen, W; Wells, R D

    1980-01-01

    The 1H NMR spectrum of a 12 base pair DNA restriction fragment has been measured at 300 and 600 MHz and resonances from over 70 protons are individually resolved. Relaxation rate measurements have been carried out at 300 MHz and compared with the theoretical predictions obtained using an isotropic rigid rotor model with coordinates derived from a Dreiding model of DNA. The model gives results that are in excellent agreement with experiment for most protons when a 7 nsec rotational correlation time is used, although agreement is improved for certain base protons by using a shorter correlation time for the sugar group, or by increasing the sugar-base interproton distances. A comparison of non-selective and selective spin-lattice relaxation rates for carbon bound protons indicates that there is extensive spin diffusion even in this short DNA fragment. Examination of the spin-spin relaxation rates for the same type of proton on different base pairs reveals little sequence effect on conformation. PMID:6258152

  20. Magnetic properties and pairing tendencies of the iron-based superconducting ladder BaFe2S3: Combined ab initio and density matrix renormalization group study

    DOE PAGES

    Patel, Niravkumar D.; Nocera, Alberto; Alvarez, Gonzalo; Arita, Ryotaro; Moreo, Adriana; Dagotto, Elbio

    2016-08-10

    The recent discovery of superconductivity under high pressure in the two-leg ladder compound BaFe2S3 [H. Takahashi et al., Nat. Mater. 14, 1008 (2015)] opens a broad avenue of research, because it represents the first report of pairing tendencies in a quasi-one-dimensional iron-based high-critical-temperature superconductor. Similarly, as in the case of the cuprates, ladders and chains can be far more accurately studied using many-body techniques and model Hamiltonians than their layered counterparts, particularly if several orbitals are active. In this publication, we derive a two-orbital Hubbard model from first principles that describes individual ladders of BaFe2S3. The model is studied withmore » the density matrix renormalization group. These first reported results are exciting for two reasons: (i) at half-filling, ferromagnetic order emerges as the dominant magnetic pattern along the rungs of the ladder, and antiferromagnetic order along the legs, in excellent agreement with neutron experiments; and (ii) with hole doping, pairs form in the strong coupling regime, as found by studying the binding energy of two holes doped on the half-filled system. In addition, orbital selective Mott phase characteristics develop with doping, with only oneWannier orbital receiving the hole carriers while the other remains half-filled. Lastly, these results suggest that the analysis of models for iron-based two-leg ladders could clarify the origin of pairing tendencies and other exotic properties of iron-based high-critical-temperature superconductors in general.« less

  1. Magnetic properties and pairing tendencies of the iron-based superconducting ladder BaFe2S3 : Combined ab initio and density matrix renormalization group study

    NASA Astrophysics Data System (ADS)

    Patel, Niravkumar D.; Nocera, Alberto; Alvarez, Gonzalo; Arita, Ryotaro; Moreo, Adriana; Dagotto, Elbio

    2016-08-01

    The recent discovery of superconductivity under high pressure in the two-leg ladder compound BaFe2S3 [H. Takahashi et al., Nat. Mater. 14, 1008 (2015), 10.1038/nmat4351] opens a broad avenue of research, because it represents the first report of pairing tendencies in a quasi-one-dimensional iron-based high-critical-temperature superconductor. Similarly, as in the case of the cuprates, ladders and chains can be far more accurately studied using many-body techniques and model Hamiltonians than their layered counterparts, particularly if several orbitals are active. In this publication, we derive a two-orbital Hubbard model from first principles that describes individual ladders of BaFe2S3 . The model is studied with the density matrix renormalization group. These first reported results are exciting for two reasons: (i) at half-filling, ferromagnetic order emerges as the dominant magnetic pattern along the rungs of the ladder, and antiferromagnetic order along the legs, in excellent agreement with neutron experiments; and (ii) with hole doping, pairs form in the strong coupling regime, as found by studying the binding energy of two holes doped on the half-filled system. In addition, orbital selective Mott phase characteristics develop with doping, with only one Wannier orbital receiving the hole carriers while the other remains half-filled. These results suggest that the analysis of models for iron-based two-leg ladders could clarify the origin of pairing tendencies and other exotic properties of iron-based high-critical-temperature superconductors in general.

  2. Novel single base-pair deletion in exon 1 of XK gene leading to McLeod syndrome with chorea, muscle wasting, peripheral neuropathy, acanthocytosis and haemolysis.

    PubMed

    Wiethoff, Sarah; Xiromerisiou, Georgia; Bettencourt, Conceição; Kioumi, Anna; Tsiptsios, Iakovos; Tychalas, Athanasios; Evaggelia, Markousi; George, Kaltsounis; Makris, Vasileios; Hardy, John; Houlden, Henry

    2014-04-15

    We present a 70-year-old male patient of Greek origin with choreatic movements of the tongue and face, lower limb muscle weakness, peripheral neuropathy, elevated creatinephosphokinase (CPK), acanthocytosis and haemolysis in the absence of Kell RBC antigens with an additional Factor IX-deficiency. Genetic testing for mutations in the three exons of the XK gene revealed a previously unreported hemizygous single base-pair frameshift deletion at exon 1 (c.229delC, p.Leu80fs). In conclusion, we hereby describe a rare phenotype of a patient with McLeod syndrome which was discovered coincidentally during routine blood group testing and consecutively genetically confirmed.

  3. Electron-hole pair mechanism for the magnetic field effect in organic light emitting diodes based on poly(paraphenylene vinylene)

    NASA Astrophysics Data System (ADS)

    Bagnich, S. A.; Niedermeier, U.; Melzer, C.; Sarfert, W.; von Seggern, H.

    2009-12-01

    We investigated the magnetic field effect (MFE) on current and electroluminescence in organic light emitting diodes based on poly(paraphenylene vinylene). The MFE was strictly positive in the full range of device operation and showed nonmonotonic dependencies on applied voltage and temperature. Furthermore, the MFE on current obtained in bipolar devices was significantly larger than in hole-dominated devices. We discuss our results in the framework of an electron-hole pair model and show that the model can explain all functional dependencies observed in our devices.

  4. Escherichia coli RNA-Polymerase Binding Sites on DNA Are Only 14 Base Pairs Long and Are Located between Sequences That Are Very Rich in A+T

    PubMed Central

    Giacomoni, Paolo U.; Le Talaer, Jean Yves; Le Pecq, Jean Bernard

    1974-01-01

    E. coli DNA-dependent RNA-polymerase binding sites on DNAs of T5, T7, and lambda coliphages have been isolated according to three different methods in order to analyze the binding sites themselves as well as the nearest neighboring regions. It is shown that the binding sites are regions that are rather rich in G+C, are about 14 base pairs long and are located between DNA sequences highly enriched in A+T. The biological implications of this result are discussed. PMID:4528552

  5. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.

    PubMed

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism. PMID:26791911

  6. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

    PubMed Central

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine–pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism. PMID:26791911

  7. In vivo dynamics of enterovirus protease revealed by fluorescence resonance emission transfer (FRET) based on a novel FRET pair

    SciTech Connect

    Hsu, Y.-Y.; Liu, Y.-N.; Wang Wenyen; Kao, Fu-Jen; Kung, S.-H. . E-mail: szkung@ym.edu.tw

    2007-02-23

    An in vivo protease assay suitable for analysis by fluorescence resonance energy transfer (FRET) was developed on the basis of a novel FRET pair. The specifically designed fusion substrate consists of green fluorescent protein 2 (GFP{sup 2})-peptide-red fluorescent protein 2 (DsRed2), with a cleavage motif for the enterovirus 2A protease (2A{sup pro}) embedded within the peptide region. FRET can be readily visualized in real-time from cells expressing the fusion substrate until a proteolytic cleavage by 2A{sup pro} from the input virus. The level of FRET decay is a function of the amount and infection duration of the inoculated virus as measured by a fluorometer assay. The FRET biosensor also responded well to other related enteroviruses but not to a phylogenetically distant virus. Western blot analysis confirmed the physical cleavage of the fusion substrate upon the infections. The study provides proof of principle for applying the FRET technology to diagnostics, screening procedures, and cell biological research.

  8. Compact Optical Fiber 3D Shape Sensor Based on a Pair of Orthogonal Tilted Fiber Bragg Gratings.

    PubMed

    Feng, Dingyi; Zhou, Wenjun; Qiao, Xueguang; Albert, Jacques

    2015-01-01

    In this work, a compact fiber-optic 3D shape sensor consisting of two serially connected 2° tilted fiber Bragg gratings (TFBGs) is proposed, where the orientations of the grating planes of the two TFBGs are orthogonal. The measurement of the reflective transmission spectrum from the pair of TFBGs was implemented by Fresnel reflection of the cleaved fiber end. The two groups of cladding mode resonances in the reflection spectrum respond differentially to bending, which allows for the unique determination of the magnitude and orientation of the bend plane (i.e. with a ± 180 degree uncertainty). Bending responses ranging from -0.33 to + 0.21 dB/m(-1) (depending on orientation) are experimentally demonstrated with bending from 0 to 3.03 m(-1). In the third (axial) direction, the strain is obtained directly by the shift of the TFBG Bragg wavelengths with a sensitivity of 1.06 pm/με. PMID:26617191

  9. Compact Optical Fiber 3D Shape Sensor Based on a Pair of Orthogonal Tilted Fiber Bragg Gratings

    PubMed Central

    Feng, Dingyi; Zhou, Wenjun; Qiao, Xueguang; Albert, Jacques

    2015-01-01

    In this work, a compact fiber-optic 3D shape sensor consisting of two serially connected 2° tilted fiber Bragg gratings (TFBGs) is proposed, where the orientations of the grating planes of the two TFBGs are orthogonal. The measurement of the reflective transmission spectrum from the pair of TFBGs was implemented by Fresnel reflection of the cleaved fiber end. The two groups of cladding mode resonances in the reflection spectrum respond differentially to bending, which allows for the unique determination of the magnitude and orientation of the bend plane (i.e. with a ± 180 degree uncertainty). Bending responses ranging from −0.33 to + 0.21 dB/m−1 (depending on orientation) are experimentally demonstrated with bending from 0 to 3.03 m−1. In the third (axial) direction, the strain is obtained directly by the shift of the TFBG Bragg wavelengths with a sensitivity of 1.06 pm/με. PMID:26617191

  10. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

    NASA Astrophysics Data System (ADS)

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

  11. Evidence for habitat partitioning based on adaptation to environmental light in a pair of sympatric lizard species.

    PubMed Central

    Leal, Manuel; Fleishman, Leo J

    2002-01-01

    Terrestrial habitats exhibit a variety of light environments. If species exhibit evolutionary adaptations of their visual system or signals to habitat light conditions, then these conditions can directly influence the structure of communities. We evaluated habitat light characteristics and visual-signal design in a pair of sympatric species of lizards: Anolis cooki and Anolis cristatellus. We found that each species occupies a distinct microhabitat with respect to light intensity and spectral quality. We measured the relative retinal spectral sensitivity and found significant differences between the species that correlate with differences in habitat spectral quality. We measured the spectral reflectance of the dewlaps (colourful throat fans used in communication), and found that the A. cooki dewlap reflects little ultraviolet (UV), while that of A. cristatellus reflects strongly in the UV. For both species downwelling light (irradiance) is rich in UV. However the background light (radiance) is rich in UV for A. cooki, but low in UV for A. cristatellus. Thus, the dewlap of each species creates a high contrast with the background in the UV. Our findings strongly suggest that these two species are partitioning their habitat through specializations of the visual system and signal design to microhabitat light conditions. PMID:11886622

  12. Pair Excitations in Fermi Fluids

    NASA Astrophysics Data System (ADS)

    Böhm, Helga M.; Krotscheck, Eckhard; Schörkhuber, Karl; Springer, Josef

    2006-09-01

    We present a theory of multi-pair excitations in strongly interacting Fermi systems. Based on an equations-of-motion approach for time-dependent pair correlations it leads to a qualitatively new structure of the density-density response function. Our theory reduces to both, i) the "correlated" random-phase approximation (RPA) for fermions if the two-pair excitations are ignored, and ii) the correlated Brillouin-Wigner perturbation theory for bosons in the appropriate limit. The theory preserves the two first energy-weighted sum rules. A familiar problem of the standard RPA is that its zero-sound mode is energetically much higher than found in experiments. The popular cure of introducing an average effective mass in the Lindhard function violates sum rules and describes the physics incorrectly. We demonstrate that the inclusion of correlated pair excitations gives the correct dispersion. As in 4He, a modification of the effective mass is unnecessary also in 3He.

  13. Can an Excess Electron Localise on a Purine Moiety in the Adenine-thymine Watson-Crick Base Pair? A Computational Study

    SciTech Connect

    Mazurkiewicz, Kamil; Haranczyk, Maciej; Gutowski, Maciej S.; Rak, Janusz

    2007-04-17

    The electron affinity and the propensity to electron-induced proton transfer (PT) of hydrogen-bonded complexes between the Watson–Crick adenine–thymine pair (AT) and simple organic acid (HX), attached to adenine in the Hoogsteen-type configuration, were studied at the B3LYP/6-31+G** level. Although the carboxyl group is deprotonated at physiological pH, its neutral form, COOH, resembles the peptide bond or the amide fragment in the side chain of asparagine (Asn) or glutamine (Gln). Thus, these complexes mimic the interaction between the DNA environment (e.g., proteins) and nucleobase pairs incorporated in the biopolymer. Electron attachment is thermodynamically feasible and adiabatic electron affinities range from 0.41 to 1.28 eV, while the vertical detachment energies of the resulting anions span the range of 0.39 –2.88 eV. Low-energy activation barriers separate the anionic minima: aHX(AT) from the more stable single-PT anionic geometry, aHX(AT)-SPT, and aHX(AT)-SPT from the double-PT anionic geometry, aHX(AT)-DPT. Interaction between the adenine of the Watson–Crick AT base pair with an acidic proton donor probably counterbalances the larger EA of isolated thymine, as SOMO is almost evenly delocalized over both types of nucleic bases in the aHX(AT) anions. Moreover, as a result of PT the excess electron localizes entirely on adenine. Thus, in DNA interacting with its physiological environment, damage induced by low-energy electrons could begin, contrary to the current view, with the formation of purine anions, which are not formed in isolated DNA because of the greater stability of anionic pyrimidines.

  14. Can an excess electron localize on a purine moiety in the adenine-thymine Watson-Crick base pair? A computational study

    NASA Astrophysics Data System (ADS)

    Mazurkiewicz, Kamil; Harańczyk, Maciej; Gutowski, Maciej; Rak, Janusz

    The electron affinity and the propensity to electron-induced proton transfer (PT) of hydrogen-bonded complexes between the Watson-Crick adenine-thymine pair (AT) and simple organic acid (HX), attached to adenine in the Hoogsteen-type configuration, were studied at the B3LYP/6-31+G** level. Although the carboxyl group is deprotonated at physiological pH, its neutral form, COOH, resembles the peptide bond or the amide fragment in the side chain of asparagine (Asn) or glutamine (Gln). Thus, these complexes mimic the interaction between the DNA environment (e.g., proteins) and nucleobase pairs incorporated in the biopolymer. Electron attachment is thermodynamically feasible and adiabatic electron affinities range from 0.41 to 1.28 eV, while the vertical detachment energies of the resulting anions span the range of 0.39-2.88 eV. Low-energy activation barriers separate the anionic minima: aHX(AT) from the more stable single-PT anionic geometry, aHX(AT)-SPT, and aHX(AT)-SPT from the double-PT anionic geometry, aHX(AT)-DPT. Interaction between the adenine of the Watson-Crick AT base pair with an acidic proton donor probably counterbalances the larger EA of isolated thymine, as SOMO is almost evenly delocalized over both types of nucleic bases in the aHX(AT) anions. Moreover, as a result of PT the excess electron localizes entirely on adenine. Thus, in DNA interacting with its physiological environment, damage induced by low-energy electrons could begin, contrary to the current view, with the formation of purine anions, which are not formed in isolated DNA because of the greater stability of anionic pyrimidines.0

  15. Contribution of intrinsic motoneuron properties to discharge hysteresis and its estimation based on paired motor unit recordings: a simulation study.

    PubMed

    Powers, Randall K; Heckman, C J

    2015-07-01

    Motoneuron activity is strongly influenced by the activation of persistent inward currents (PICs) mediated by voltage-gated sodium and calcium channels. However, the amount of PIC contribution to the activation of human motoneurons can only be estimated indirectly. Simultaneous recordings of pairs of motor units have been used to provide an estimate of the PIC contribution by using the firing rate of the lower threshold unit to provide an estimate of the common synaptic drive to both units, and the difference in firing rate (ΔF) of this lower threshold unit at recruitment and de-recruitment of the higher threshold unit to estimate the PIC contribution to activation of the higher threshold unit. It has recently been suggested that a number of factors other than PIC can contribute to ΔF values, including mechanisms underlying spike frequency adaptation and spike threshold accommodation. In the present study, we used a set of compartmental models representing a sample of 20 motoneurons with a range of thresholds to investigate how several different intrinsic motoneuron properties can potentially contribute to variations in ΔF values. We drove the models with linearly increasing and decreasing noisy conductance commands of different rate of rise and duration and determined the influence of different intrinsic mechanisms on discharge hysteresis (the difference in excitatory drive at recruitment and de-recruitment) and ΔF. Our results indicate that, although other factors can contribute, variations in discharge hysteresis and ΔF values primarily reflect the contribution of dendritic PICs to motoneuron activation.

  16. Two-sample density-based empirical likelihood ratio tests based on paired data, with application to a treatment study of attention-deficit/hyperactivity disorder and severe mood dysregulation.

    PubMed

    Vexler, Albert; Tsai, Wan-Min; Gurevich, Gregory; Yu, Jihnhee

    2012-07-30

    It is a common practice to conduct medical trials to compare a new therapy with a standard-of-care based on paired data consisted of pre- and post-treatment measurements. In such cases, a great interest often lies in identifying treatment effects within each therapy group and detecting a between-group difference. In this article, we propose exact nonparametric tests for composite hypotheses related to treatment effects to provide efficient tools that compare study groups utilizing paired data. When correctly specified, parametric likelihood ratios can be applied, in an optimal manner, to detect a difference in distributions of two samples based on paired data. The recent statistical literature introduces density-based empirical likelihood methods to derive efficient nonparametric tests that approximate most powerful Neyman-Pearson decision rules. We adapt and extend these methods to deal with various testing scenarios involved in the two-sample comparisons based on paired data. We show that the proposed procedures outperform classical approaches. An extensive Monte Carlo study confirms that the proposed approach is powerful and can be easily applied to a variety of testing problems in practice. The proposed technique is applied for comparing two therapy strategies to treat children's attention deficit/hyperactivity disorder and severe mood dysregulation. PMID:22714114

  17. Crystallization and preliminary X-ray diffraction analysis of the Bacillus subtilis replication termination protein in complex with the 37-base-pair TerI-binding site

    SciTech Connect

    Vivian, J. P.; Porter, C.; Wilce, J. A.; Wilce, M. C. J.

    2006-11-01

    A preparation of replication terminator protein (RTP) of B. subtilis and a 37-base-pair TerI sequence (comprising two binding sites for RTP) has been purified and crystallized. The replication terminator protein (RTP) of Bacillus subtilis binds to specific DNA sequences that halt the progression of the replisome in a polar manner. These terminator complexes flank a defined region of the chromosome into which they allow replication forks to enter but not exit. Forcing the fusion of replication forks in a specific zone is thought to allow the coordination of post-replicative processes. The functional terminator complex comprises two homodimers each of 29 kDa bound to overlapping binding sites. A preparation of RTP and a 37-base-pair TerI sequence (comprising two binding sites for RTP) has been purified and crystallized. A data set to 3.9 Å resolution with 97.0% completeness and an R{sub sym} of 12% was collected from a single flash-cooled crystal using synchrotron radiation. The diffraction data are consistent with space group P622, with unit-cell parameters a = b = 118.8, c = 142.6 Å.

  18. The effect of the glycosylation position on the base pairing and supramolecular structure of the 5‧-deoxyribosyl Janus-type AT nucleosides

    NASA Astrophysics Data System (ADS)

    Zhou, Xinglong; Liu, Jiang; Guo, Xiurong; Meng, Liying; Chu, Liangyin; Chen, Qianming; Zhao, Hang; He, Yang

    2015-11-01

    The intrinsic structural diversity of the nucleosides is one of the essential properties for their wide participation in myriads of chemical or biochemical processes. Two unique regio-isomeric Janus-type AT nucleosides with the 5‧-deoxyribose attached on N1 or N3 position has been synthesized through Vorbrueggen or transglycosylation reactions. These two isomers display different supramolecular morphologies in solution state from their N8 glycosylated counterpart. The underneath structural details of the N3 glycosylated isomer were revealed by the single-crystal X-ray analysis. In addition to a novel base pair pattern was identified which is entirely different from the reverse Watson-Crick base pair adopted by its N8 isomer, an interesting water-filled columnar nanotuble-like structure was also found in its solid state. This study not only enriches the structural varieties of AT Janus-type nucleosides, but also provides specific information concerning the effect of the sugar glycosylation position on the properties of these new type of pyrimido[4,5-d]pyrimidine nucleosides.

  19. Tube Stent-Grafts for Infrarenal Aortic Aneurysm: A Matched-Paired Analysis Based on EUROSTAR Data

    SciTech Connect

    Ruppert, Volker Leurs, Lina J.; Hobo, Roel; Buth, Jacob; Rieger, Johannes; Umscheid, Thomas

    2007-07-15

    Objective. Tube stent-grafts for treatment of infrarenal aortic aneurysms (AAAs) are a nearly forgotten concept. For focal aortic pathologies tube stent-grafts may be a treatment option. We have performed a retrospective matched-paired analysis of the EUROSTAR registry regarding the outcome of tube vs. bifurcated stent-grafts for AAA. Tapered aortomonoiliac stent-grafts were not the objective of this study. Materials and methods. From July 1997 to June 2006, 7581 patients who underwent an endovascular AAA repair were entered in the EUROSTAR registry by 164 centers. One hundred fifty-three patients were treated with tube stent-grafts. For each of these 153 patients we selected one patient from a bifurcated stent-graft group (BGG-original, 7428 patients) matched according to gender, ASA, age, AAA diameter, and type of anesthesia. Differences in preoperative details between the two study groups were analyzed using chi-square test for discrete variables and Wilcoxon rank-sum test for continuous variables. Multivariate logistic regression analysis was performed on early complications. Midterm outcomes (>30 days) were analyzed by Kaplan-Meier and multivariate Cox proportional hazard model. Results. The duration of the procedure was shorter in the tube stent-graft group (TGG; 102.3 {+-} 52.2) than in BGG (128.3 {+-} 55.0; p 0.0002). Type II endoleak was less frequent in TGG (4.0%; mean follow-up, 23.12 {+-} 23.9 months) than in BGG (14.3%; mean follow-up, 20.77 {+-} 20.0 months; p = 0.0394). Type I endoleaks and migration were distributed equally, without significant differences between the groups. Combined 30-day and late mortality was higher for TGG (p = 0.0346) and was obviously not aneurysm related. Conclusions. We conclude that after selection of patients, tube stent-grafts for infrarenal aortic repair can be performed with great safety regarding endoleaks and migration. The combined higher 30-day mortality and non-aneurysm-related mortality during follow-up were

  20. Analysis and Simulation of the Simplified Aircraft-Based Paired Approach Concept With the ALAS Alerting Algorithm in Conjunction With Echelon and Offset Strategies

    NASA Technical Reports Server (NTRS)

    Torres-Pomales, Wilfredo; Madden, Michael M.; Butler, Rickey W.; Perry, Raleigh B.

    2014-01-01

    This report presents analytical and simulation results of an investigation into proposed operational concepts for closely spaced parallel runways, including the Simplified Aircraft-based Paired Approach (SAPA) with alerting and an escape maneuver, MITRE?s echelon spacing and no escape maneuver, and a hybrid concept aimed at lowering the visibility minima. We found that the SAPA procedure can be used at 950 ft separations or higher with next-generation avionics and that 1150 ft separations or higher is feasible with current-rule compliant ADS-B OUT. An additional 50 ft reduction in runway separation for the SAPA procedure is possible if different glideslopes are used. For the echelon concept we determined that current generation aircraft cannot conduct paired approaches on parallel paths using echelon spacing on runways less than 1400 ft apart and next-generation aircraft will not be able to conduct paired approach on runways less than 1050 ft apart. The hybrid concept added alerting and an escape maneuver starting 1 NM from the threshold when flying the echelon concept. This combination was found to be effective, but the probability of a collision can be seriously impacted if the turn component of the escape maneuver has to be disengaged near the ground (e.g. 300 ft or below) due to airport buildings and surrounding terrain. We also found that stabilizing the approach path in the straight-in segment was only possible if the merge point was at least 1.5 to 2 NM from the threshold unless the total system error can be sufficiently constrained on the offset path and final turn.

  1. Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0

    PubMed Central

    2010-01-01

    Background The growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling. Findings GeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations. Conclusions The web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind. PMID:20178631

  2. Pairing forces in nuclei

    SciTech Connect

    Chasman, R.R.

    1996-12-31

    In this contribution, the author mentions some features of pairing forces that are unique to nuclei and cover some areas of major interest in nuclear structure research, that involve pairing. At the level of most nuclear structure studies, nuclei are treated as consisting of two kinds of fermions (protons and neutrons) in a valence space with rather few levels. These features give rise to unique aspects of pairing forces in nuclei: (1) n-p pairing in T = 0 as well as the usual T = 1 pairing that is characteristic of like fermions; (2) a need to correct pairing calculations for the (1/N) effects that can typically be neglected in superconducting solids. An issue of current concern is the nature of the pairing interaction: several recent studies suggest a need for a density dependent form of the pairing interaction. There is a good deal of feedback between the questions of accurate calculations of pairing interactions and the form and magnitude of the pairing interaction. Finally, the authors discuss some many-body wave functions that are a generalization of the BCS wave function form, and apply them to a calculation of energy level spacings in superdeformed rotational bands.

  3. Five-State Molecular Shuttling of a Pair of [2]Rotaxanes: Distinct Outputs in Response to Acid and Base Stimuli.

    PubMed

    Ueda, Masahiro; Terazawa, Shoya; Deguchi, Yasuaki; Kimura, Masaki; Matsubara, Naoki; Miyagawa, Shinobu; Kawasaki, Tsuneomi; Tokunaga, Yuji

    2016-08-19

    In this study we synthesized two acid-/base-controllable [2]rotaxanes featuring aminodiazobenzene and aminocoumarin units, respectively, as chromophores and dibenzo[24]crown-8 and dibenzo[25]crown-8 units, respectively, as their macrocyclic components. Each [2]rotaxane contained N-alkylarylamine (ammonium) and N,N-dialkylamine (ammonium) centers as binding sites for their crown ether components. The absorption patterns of the chromophores were dependent on the position of the encircling macrocyclic component and the degree of protonation, with three distinct states (under acidic, neutral, and basic conditions) evident for each [2]rotaxane. The mixed [2]rotaxane system displayed stepwise and independent molecular shuttling behavior based on the degree of protonation of the amino groups in response to both the amount and strength of added acids or bases; as such, the system provided five different absorption signals as outputs that could be read using UV/Vis spectroscopy. PMID:27355789

  4. On the time-course of adjacent and non-adjacent transposed-letter priming

    PubMed Central

    Ktori, Maria; Kingma, Brechtsje; Hannagan, Thomas; Holcomb, Phillip J.; Grainger, Jonathan

    2014-01-01

    We compared effects of adjacent (e.g., atricle-ARTICLE) and non-adjacent (e.g., actirle-ARTICLE) transposed-letter (TL) primes in an ERP study using the sandwich priming technique. TL priming was measured relative to the standard double-substitution condition. We found significantly stronger priming effects for adjacent transpositions than non-adjacent transpositions (with 2 intervening letters) in behavioral responses (lexical decision latencies), and the adjacent priming effects emerged earlier in the ERP signal, at around 200 ms post-target onset. Non-adjacent priming effects emerged about 50 ms later and were short-lived, being significant only in the 250-300 ms time-window. Adjacent transpositions on the other hand continued to produce priming in the N400 time-window (300-500 ms post-target onset). This qualitatively different pattern of priming effects for adjacent and non-adjacent transpositions is discussed in the light of different accounts of letter transposition effects, and the utility of drawing a distinction between positional flexibility and positional noise. PMID:25364497

  5. Effective Diffusion Coefficient and Controlling Process of P Diffusion in Si Based on the Pair Diffusion Models of Vacancy and Interstitial Mechanisms

    NASA Astrophysics Data System (ADS)

    Yoshida, Masayuki; Morooka, Masami; Takahashi, Manabu; Tomokage, Hajime

    2000-05-01

    Based on the pair diffusion models of vacancy and interstitial (V and I) mechanisms, the V and I components of effective P diffusion coefficient, DP^+,Veff and DP^+,Ieff, and the controlling process of P diffusion in Si are obtained. Assuming that the I mechanism is dominant, not only the I- concentration, CI^-, but also its gradient, d CI^-/d λ , is effective on DP^+,Ieff at high CP^+. DP^+,Ieff is large at d CI^-/d λ <0 and small at d CI^-/d λ >0. P+ and I- are generated by the dissociation of P-I pair. When excess I- thus generated is removed, d CI^-/d λ <0 is obtained. d CI^-/d λ <0 is also obtained by the decrease in quasi self-interstitial formation energy. Several diffusion models simulate the P diffusion profile well under an inert atmosphere. Applying the controlling process to them, the reason why they simulate the P profile well is investigated. Because all of them simulate the P profile well, it is difficult to conclude which model is correct. It is suggested that it is possible to conclude which model is correct from the P profile under oxidation at CP^+s >1× 1020 cm-3 (s: surface).

  6. Phylogeny of organisms investigated by the base-pair changes in the stem regions of small and large ribosomal subunit RNAs.

    PubMed

    Otsuka, J; Terai, G; Nakano, T

    1999-02-01

    In order to obtain the evolutionary distance data that are as purely additive as possible, we have developed a novel method for evaluating the evolutionary distances from the base-pair changes in stem regions of ribosomal RNAs (rRNAs). The application of this method to small-subunit (SSU) and large-subunit (LSU) rRNAs provides the distance data, with which both the unweighted pair group method of analysis and the neighbor-joining method give almost the same tree topology of most organisms except for some Protoctista, thermophilic bacteria, parasitic organisms, and endosymbionts. Although the evolutionary distances calculated with LSU rRNAs are somewhat longer than those with SSU rRNAs, the difference, probably due to a slight difference in functional constraint, is substantially decreased when the distances are converted into the divergence times of organisms by the measure of the time scale estimated in each type of rRNAs. The divergence times of main branches agree fairly well with the geological record of organisms, at least after the appearance of oxygen-releasing photosynthesis, although the divergence times of Eukaryota, Archaebacteria, and Eubacteria are somewhat overestimated in comparison with the geological record of Earth formation. This result is explained by considering that the mutation rate is determined by the accumulation of misrepairs for DNA damage caused by radiation and that the effect of radiation had been stronger before the oxygen molecules became abundant in the atmosphere of the Earth.

  7. Population based study of prevalence of islet cell autoantibodies in monozygotic and dizygotic Danish twin pairs with insulin dependent diabetes mellitus.

    PubMed Central

    Petersen, J. S.; Kyvik, K. O.; Bingley, P. J.; Gale, E. A.; Green, A.; Dyrberg, T.; Beck-Nielsen, H.

    1997-01-01

    OBJECTIVE: To study the comparative importance of environment and genes in the development of islet cell autoimmunity associated with insulin dependent diabetes mellitus. DESIGN: Population based study of diabetic twins. SETTING: Danish population. SUBJECTS: 18 monozygotic and 36 dizygotic twin pairs with one or both partners having insulin dependent diabetes. MAIN OUTCOME MEASURES: Presence of islet cell antibodies, insulin autoantibodies, and autoantibodies to glutamic acid decarboxylase (GAD65) in serum samples from twin pairs 10 years (range 0-30 years) and 9.5 years (2-30 years) after onset of disease. RESULTS: In those with diabetes the prevalence of islet cell antibodies, insulin autoantibodies, and autoantibodies to glutamic acid decarboxylase in the 26 monozygotic twins was 38%, 85%, and 92%, respectively, and in the dizygotic twins was 57%, 70%, and 57%, respectively. In those without diabetes the proportions were 20%, 50%, and 40% in the 10 monozygotic twins and 26%, 49%, and 40% in the 35 dizygotic twins. CONCLUSION: There is no difference between the prevalence of islet cell autoantibodies in dizygotic and monozygotic twins without diabetes, suggesting that islet cell autoimmunity is environmentally rather than genetically determined. Furthermore, the prevalence of islet cell antibodies was higher in the non-diabetic twins than in other first degree relatives of patients with insulin dependent diabetes. This implies that the prenatal or early postnatal period during which twins are exposed to the same environment, in contrast with that experienced by first degree relatives, is of aetiological importance. PMID:9169400

  8. Phylogeny of organisms investigated by the base-pair changes in the stem regions of small and large ribosomal subunit RNAs.

    PubMed

    Otsuka, J; Terai, G; Nakano, T

    1999-02-01

    In order to obtain the evolutionary distance data that are as purely additive as possible, we have developed a novel method for evaluating the evolutionary distances from the base-pair changes in stem regions of ribosomal RNAs (rRNAs). The application of this method to small-subunit (SSU) and large-subunit (LSU) rRNAs provides the distance data, with which both the unweighted pair group method of analysis and the neighbor-joining method give almost the same tree topology of most organisms except for some Protoctista, thermophilic bacteria, parasitic organisms, and endosymbionts. Although the evolutionary distances calculated with LSU rRNAs are somewhat longer than those with SSU rRNAs, the difference, probably due to a slight difference in functional constraint, is substantially decreased when the distances are converted into the divergence times of organisms by the measure of the time scale estimated in each type of rRNAs. The divergence times of main branches agree fairly well with the geological record of organisms, at least after the appearance of oxygen-releasing photosynthesis, although the divergence times of Eukaryota, Archaebacteria, and Eubacteria are somewhat overestimated in comparison with the geological record of Earth formation. This result is explained by considering that the mutation rate is determined by the accumulation of misrepairs for DNA damage caused by radiation and that the effect of radiation had been stronger before the oxygen molecules became abundant in the atmosphere of the Earth. PMID:9929391

  9. Ion pair-based dispersive liquid-liquid microextraction followed by high performance liquid chromatography as a new method for determining five folate derivatives in foodstuffs.

    PubMed

    Nojavan, Yones; Kamankesh, Marzieh; Shahraz, Farzaneh; Hashemi, Maryam; Mohammadi, Abdorreza

    2015-05-01

    A novel technique for simultaneous determination of five folate derivatives in various food matrices was developed by ion pair-based dispersive liquid-liquid microextraction (IP-DLLME) combined with high-performance liquid chromatography (HPLC). In the proposed method, N-methyl-N,N-dioctyloctan-1-ammonium chloride (aliquat-336) was used as an ion-pair reagent. Effective variables of microextraction process were optimized. Under optimum conditions, the method yielded a linear calibration curve ranging from 1-200 ng g(-1) with correlation coefficients (r(2)) higher than 0.98. The relative standard deviation for the seven analyses was 5.2-7.4%. Enrichment factors for the five folates ranged between 108-135. Limits of detection were 2-4.1 ng g(-1). A comparison of this method with other methods described that the new proposed method is rapid and accurate, and gives very good enrichment factors and detection limits for determining five folate derivatives. The newly developed method was successfully applied for the determination of five folate derivatives in wheat flour, egg yolk and orange juice samples.

  10. Matched-pair classification

    SciTech Connect

    Theiler, James P

    2009-01-01

    Following an analogous distinction in statistical hypothesis testing, we investigate variants of machine learning where the training set comes in matched pairs. We demonstrate that even conventional classifiers can exhibit improved performance when the input data has a matched-pair structure. Online algorithms, in particular, converge quicker when the data is presented in pairs. In some scenarios (such as the weak signal detection problem), matched pairs can be generated from independent samples, with the effect not only doubling the nominal size of the training set, but of providing the structure that leads to better learning. A family of 'dipole' algorithms is introduced that explicitly takes advantage of matched-pair structure in the input data and leads to further performance gains. Finally, we illustrate the application of matched-pair learning to chemical plume detection in hyperspectral imagery.

  11. How subaerial salt extrusions influence water quality in adjacent aquifers

    NASA Astrophysics Data System (ADS)

    Mehdizadeh, Razieh; Zarei, Mehdi; Raeisi, Ezzat

    2015-12-01

    Brines supplied from salt extrusions cause significant groundwater salinization in arid and semi-arid regions where salt rock is exposed to dissolution by episodic rainfalls. Here we focus on 62 of the 122 diapirs of Hormuz salt emergent in the southern Iran. To consider managing the degradation effect that salt extrusions have on the quality of adjoining aquifers, it is first necessary to understand how they influence adjacent water resources. We evaluate here the impacts that these diapirs have on adjacent aquifers based on investigating their geomorphologies, geologies, hydrologies and hydrogeologies. The results indicate that 28/62 (45%) of our sample of salt diapirs have no significant impact on the quality of groundwater in adjoining aquifers (namely Type N), while the remaining 34/62 (55%) degrade nearby groundwater quality. We offer simple conceptual models that account for how brines flowing from each of these types of salt extrusions contaminate adjacent aquifers. We identify three main mechanisms that lead to contamination: surface impact (Type A), subsurface intrusion (Type B) and indirect infiltration (Type C). A combination of all these mechanisms degrades the water quality in nearby aquifers in 19/62 (31%) of the salt diapirs studied. Having characterized the mechanism(s) by which each diapir affects the adjacent aquifer, we suggest a few possible remediation strategies to be considered. For instance, engineering the surface runoff of diapirs Types A and C into nearby evaporation basins would improve groundwater quality.

  12. Paired watershed study design

    SciTech Connect

    Clausen, J.C.; Spooner, J.

    1993-09-01

    The purpose of the fact sheet is to describe the paired watershed approach for conducting nonpoint source (NPS) water quality studies. The basic approach requires a minimum of two watersheds - control and treatment - and two periods of study - calibration and treatment. The basis of the paired watershed approach is that there is a quantifiable relationship between paired water quality data for the two watersheds, and that this relationship is valid until a major change is made in one of the watersheds.

  13. Vortex pairs on surfaces

    SciTech Connect

    Koiller, Jair

    2009-05-06

    A pair of infinitesimally close opposite vortices moving on a curved surface moves along a geodesic, according to a conjecture by Kimura. We outline a proof. Numerical simulations are presented for a pair of opposite vortices at a close but nonzero distance on a surface of revolution, the catenoid. We conjecture that the vortex pair system on a triaxial ellipsoid is a KAM perturbation of Jacobi's geodesic problem. We outline some preliminary calculations required for this study. Finding the surfaces for which the vortex pair system is integrable is in order.

  14. Pairing Beyond BCS

    NASA Astrophysics Data System (ADS)

    Volya, Alexander; Zelevinsky, Vladimir

    2013-01-01

    We concentrate on the specifics of the nuclear pairing problem from the standpoint of the BCS approach. We consider the properties of nuclear pairing which usually are not discussed in standard texts: how good is the BCS theory in nuclear context compared to the exact large-scale diagonalization, whether it can be improved by the particle number conservation, how to mark the phase transition regions in a mesoscopic system like a nucleus, how may effective many-body forces influence the formation and structure of the pairing condensate, what effect the decay instability has on the paired nuclear structure, etc.

  15. How semantic biases in simple adjacencies affect learning a complex structure with non-adjacencies in AGL: a statistical account

    PubMed Central

    Poletiek, Fenna H.; Lai, Jun

    2012-01-01

    A major theoretical debate in language acquisition research regards the learnability of hierarchical structures. The artificial grammar learning methodology is increasingly influential in approaching this question. Studies using an artificial centre-embedded AnBn grammar without semantics draw conflicting conclusions. This study investigates the facilitating effect of distributional biases in simple AB adjacencies in the input sample—caused in natural languages, among others, by semantic biases—on learning a centre-embedded structure. A mathematical simulation of the linguistic input and the learning, comparing various distributional biases in AB pairs, suggests that strong distributional biases might help us to grasp the complex AnBn hierarchical structure in a later stage. This theoretical investigation might contribute to our understanding of how distributional features of the input—including those caused by semantic variation—help learning complex structures in natural languages. PMID:22688639

  16. Synthesis and monitored selection of nucleotide surrogates for binding T:A base pairs in homopurine–homopyrimidine DNA triple helices

    PubMed Central

    Mokhir, Andriy A.; Connors, William H.; Richert, Clemens

    2001-01-01

    A total of 16 oligodeoxyribonucleotides of general sequence 5′-TCTTCTZTCTTTCT-3′, where Z denotes an N-acyl-N-(2-hydroxyethyl)glycine residue, were prepared via solid phase synthesis. The ability of these oligonucleotides to form triplexes with the duplex 5′-AGAAGATAGAAAGA-HEG-TCTTTCTATCTTCT-3′, where HEG is a hexaethylene glycol linker, was tested. In these triplexes, an ‘interrupting’ T:A base pair faces the Z residue in the third strand. Among the acyl moieties of Z tested, an anthraquinone carboxylic acid residue linked via a glycinyl group gave the most stable triplex, whose UV melting point was 8.4°C higher than that of the triplex with 5′-TCTTCTGTCTTTCT-3′ as the third strand. The results from exploratory nuclease selection experiments suggest that a combinatorial search for strands capable of recognizing mixed sequences by triple helix formation is feasible. PMID:11522839

  17. Probing microstructures in double-helical DNA with chiral metal complexes: Recognition of changes in base-pair propeller twisting in solution

    SciTech Connect

    Pyle, A.M.; Morii, Takashi; Barton, J.K. )

    1990-12-05

    That DNA base pairs are propeller twisted in a sequence-dependent manner has been evident only in viewing crystal structures of oligonucleotides. Here the authors report that shape-selective DNA-binding molecules can recognize and distinguish propeller twisted DNA sites in solution on the basis of shape and symmetry. Enantioselective discrimination is apparent in photocleavage by Rh(phen){sub 2}phi{sup 3+} (phen = 1,10-phenanthroline; phi = 9,10-phenanthrenequinone diimine) at 5{prime}-pyr-pyr-pur-3{prime} steps which are characterized by a high degree of differential propeller twist but not at homopyrimidine-homopurine segments. Neither isomer targets 5{prime}-pur-pyr-3{prime} steps.

  18. Study of hole pair condensation based on the SU(2) Slave-Boson approach to the t-J Hamiltonian: Temperature, momentum and doping dependences of spectral functions

    SciTech Connect

    Salk, S.H.S.; Lee, S.S.

    1999-11-01

    Based on the U(1) and SU(2) slave-boson approaches to the t-J Hamiltonian, the authors evaluate the one electron spectral functions for the hole doped high {Tc} cuprates for comparison with the angle resolved photoemission spectroscopy (ARPES) data. They find that the observed quasiparticle peak in the superconducting state is correlated with the hump which exists in the normal state. They find that the spectral weight of the quasiparticle peak increases as doping rate increases, which is consistent with observation. As a consequence of the phase fluctuation effects of the spinon and holon pairing order parameters the spectral weight of the predicted peak obtained from the SU(2) theory is found to be smaller than the one predicted from U(1) mean field theory.

  19. Nodal-line pairing with 1D-3D coupled Fermi surfaces: A model motivated by Cr-based superconductors

    NASA Astrophysics Data System (ADS)

    Wachtel, Gideon; Kim, Yong Baek

    2016-09-01

    Motivated by the recent discovery of a new family of chromium-based superconductors, we consider a two-band model, where a band of electrons dispersing only in one direction interacts with a band of electrons dispersing in all three directions. Strong 2 kf density fluctuations in the one-dimensional band induces attractive interactions between the three-dimensional electrons, which, in turn, makes the system superconducting. Solving the associated Eliashberg equations, we obtain a gap function which is peaked at the "poles" of the three-dimensional Fermi sphere, and decreases towards the "equator." When strong enough local repulsion is included, the gap actually changes sign around the equator and nodal rings are formed. These nodal rings manifest themselves in several experimentally observable quantities, some of which resemble unconventional observations in the newly discovered superconductors which motivated this work.

  20. Cyanine-based probe\\tag-peptide pair for fluorescence protein imaging and fluorescence protein imaging methods

    DOEpatents

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2010-08-17

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  1. A species-specific primer pair for distinguishing between Paramisgurnus dabryanus and Misgurnus anguillicaudatus based on mitochondrial DNA polymorphisms.

    PubMed

    Liu, Yongfu; Hou, Jilun; Wang, Guixing; Zhang, Xiaoyan; Liu, Haijin

    2016-07-01

    Paramisgurnus dabryanus and Misgurnus anguillicaudatus (family Cobitidae) are loaches with high morphological similarity. In this study, we designed primers to distinguish between Paramisgurnus dabryanus and Misgurnus anguillicaudatus based on the length differences in the mitochondrial COXII to tRNA(Lys) gene region. Samples of P. dabryanus and M. anguillicaudatus from different geographical locations were collected and amplified to verify primer specificity. The results of electrophoresis revealed the successful amplification of all P. dabryanus and M. anguillicaudatus DNA samples, which had distinct, specific-specific sizes (214 bp for P. dabryanus and 285 bp for M. anguillicaudatus). In conclusion, the new primers provide fast, reliable, and accurate identification between P. dabryanus and M. anguillicaudatus.

  2. Growing Right Onto Wellness (GROW): A Family-Centered, Community-Based Obesity Prevention Randomized Controlled Trial for Preschool Child-Parent Pairs

    PubMed Central

    Po’e, Eli K.; Heerman, William J.; Mistry, Rishi S.; Barkin, Shari L.

    2013-01-01

    Growing Right Onto Wellness (GROW) is a randomized controlled trial that tests the efficacy of a family-centered, community-based, behavioral intervention to prevent childhood obesity among preschool-aged children. Focusing on parent-child pairs, GROW utilizes a multi-level framework, which accounts for macro (i.e., built-environment) and micro (i.e., genetics) level systems that contribute to the childhood obesity epidemic. Six hundred parent-child pairs will be randomized to a 3-year healthy lifestyle intervention or a 3-year school readiness program. Eligible children are enrolled between ages 3 and 5, are from minority communities, and are not obese. The principal site for the GROW intervention is local community recreation centers and libraries. The primary outcome is childhood Body Mass Index (BMI) trajectory at the end of the three-year study period. In addition to other anthropometric measurements, mediators and moderators of growth are considered, including genetics, accelerometry, and diet recall. GROW is a staged intensity intervention, consisting of intensive, maintenance, and sustainability phases. Throughout the study, parents build skills in nutrition, physical activity, and parenting, concurrently forming new social networks. Participants are taught goal-setting, self-monitoring, and problem solving techniques to facilitate sustainable behavior change. The GROW curriculum uses low health literacy communication and social media to communicate key health messages. The control arm is administered to both control and intervention participants. By conducting this trial in public community centers, and by implementing a family-centered approach to sustainable healthy childhood growth, we aim to develop an exportable community-based intervention to address the expanding public health crisis of pediatric obesity. PMID:24012890

  3. Growing Right Onto Wellness (GROW): a family-centered, community-based obesity prevention randomized controlled trial for preschool child-parent pairs.

    PubMed

    Po'e, Eli K; Heerman, William J; Mistry, Rishi S; Barkin, Shari L

    2013-11-01

    Growing Right Onto Wellness (GROW) is a randomized controlled trial that tests the efficacy of a family-centered, community-based, behavioral intervention to prevent childhood obesity among preschool-aged children. Focusing on parent-child pairs, GROW utilizes a multi-level framework, which accounts for macro (i.e., built-environment) and micro (i.e., genetics) level systems that contribute to the childhood obesity epidemic. Six hundred parent-child pairs will be randomized to a 3-year healthy lifestyle intervention or a 3-year school readiness program. Eligible children are enrolled between ages 3 and 5, are from minority communities, and are not obese. The principal site for the GROW intervention is local community recreation centers and libraries. The primary outcome is childhood body mass index (BMI) trajectory at the end of the three-year study period. In addition to other anthropometric measurements, mediators and moderators of growth are considered, including genetics, accelerometry, and diet recall. GROW is a staged intensity intervention, consisting of intensive, maintenance, and sustainability phases. Throughout the study, parents build skills in nutrition, physical activity, and parenting, concurrently forming new social networks. Participants are taught goal-setting, self-monitoring, and problem solving techniques to facilitate sustainable behavior change. The GROW curriculum uses low health literacy communication and social media to communicate key health messages. The control arm is administered to both control and intervention participants. By conducting this trial in public community centers, and by implementing a family-centered approach to sustainable healthy childhood growth, we aim to develop an exportable community-based intervention to address the expanding public health crisis of pediatric obesity.

  4. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

    NASA Astrophysics Data System (ADS)

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F.; Neese, Frank

    2016-01-01

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate previous

  5. Red-shifted hydrogen bonds and blue-shifted van der Waals contact in the standard Watson-Crick adenine-thymine base pair.

    PubMed

    Zhou, Pan-Pan; Qiu, Wen-Yuan

    2009-09-24

    Standard Watson-Crick adenine-thymine (AT) base pair has been investigated by using the B3LYP functional with 6-31G(d, p) basis set, at which level of theory the geometrical characteristics of the AT base pair are the best in agreement with the experiment. It exhibits simultaneously red-shifted N-H...O and N-H...N hydrogen bonds as well as a blue-shifted C-H...O contact. AIM analysis suggests that the blue-shifted C-H...O contact exists as van der Waals interaction, and the electron density rho that reflects the strength of a bond has been used to explain the red- and blue-shifted. By means of NBO analysis, we report a method to estimate the effect of hyperconjugation quantitatively, which combines the electron density in the X-H (X = N, C) sigma bonding orbital with that in the sigma* antibonding orbital. The effect of structural reorganization on the origins of the red- and blue-shifted has been considered by the partial optimization, its behavior on the X-H (X = N, C) bond is quite different. Rehybridization and repolarization models are employed, and they act as bond-shortening effects. The competition between the electrostatic attractions and Pauli/nucleus repulsions is present in the two typical red-shifted N-H...O and N-H...N hydrogen bonds as well as in the blue-shifted C-H...O van der Waals contact. Electrostatic attraction between H and Y atoms (Y = O, N) is an important reason for the red shift, while the nucleus-nucleus repulsion between H and O atoms may be a factor leading to the C-H bond contraction and its blue shift. The electric field effect induced by the acceptor O atom on the C-H bond is also discussed.

  6. Sparse maps--A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory.

    PubMed

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F; Neese, Frank

    2016-01-14

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  7. Sparse maps--A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory.

    PubMed

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F; Neese, Frank

    2016-01-14

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  8. Laboratory evolution of Geobacter sulfurreducens for enhanced growth on lactate via a single-base-pair substitution in a transcriptional regulator

    PubMed Central

    Summers, Zarath M; Ueki, Toshiyuki; Ismail, Wael; Haveman, Shelley A; Lovley, Derek R

    2012-01-01

    The addition of organic compounds to groundwater in order to promote bioremediation may represent a new selective pressure on subsurface microorganisms. The ability of Geobacter sulfurreducens, which serves as a model for the Geobacter species that are important in various types of anaerobic groundwater bioremediation, to adapt for rapid metabolism of lactate, a common bioremediation amendment, was evaluated. Serial transfer of five parallel cultures in a medium with lactate as the sole electron donor yielded five strains that could metabolize lactate faster than the wild-type strain. Genome sequencing revealed that all five strains had non-synonymous single-nucleotide polymorphisms in the same gene, GSU0514, a putative transcriptional regulator. Introducing the single-base-pair mutation from one of the five strains into the wild-type strain conferred rapid growth on lactate. This strain and the five adaptively evolved strains had four to eight-fold higher transcript abundance than wild-type cells for genes for the two subunits of succinyl-CoA synthase, an enzyme required for growth on lactate. DNA-binding assays demonstrated that the protein encoded by GSU0514 bound to the putative promoter of the succinyl-CoA synthase operon. The binding sequence was not apparent elsewhere in the genome. These results demonstrate that a single-base-pair mutation in a transcriptional regulator can have a significant impact on the capacity for substrate utilization and suggest that adaptive evolution should be considered as a potential response of microorganisms to environmental change(s) imposed during bioremediation. PMID:22113376

  9. ETMB-RBF: Discrimination of Metal-Binding Sites in Electron Transporters Based on RBF Networks with PSSM Profiles and Significant Amino Acid Pairs

    PubMed Central

    Ou, Yu-Yen; Chen, Shu-An; Wu, Sheng-Cheng

    2013-01-01

    Background Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation–reduction reactions. In these oxidation–reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain. Methods We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins. Results We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88. Conclusions We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins

  10. Use of a line-pair resolution phantom for comprehensive quality assurance of electronic portal imaging devices based on fundamental imaging metrics

    SciTech Connect

    Gopal, Arun; Samant, Sanjiv S.

    2009-06-15

    Image guided radiation therapy solutions based on megavoltage computed tomography (MVCT) involve the extension of electronic portal imaging devices (EPIDs) from their traditional role of weekly localization imaging and planar dose mapping to volumetric imaging for 3D setup and dose verification. To sustain the potential advantages of MVCT, EPIDs are required to provide improved levels of portal image quality. Therefore, it is vital that the performance of EPIDs in clinical use is maintained at an optimal level through regular and rigorous quality assurance (QA). Traditionally, portal imaging QA has been carried out by imaging calibrated line-pair and contrast resolution phantoms and obtaining arbitrarily defined QA indices that are usually dependent on imaging conditions and merely indicate relative trends in imaging performance. They are not adequately sensitive to all aspects of image quality unlike fundamental imaging metrics such as the modulation transfer function (MTF), noise power spectrum (NPS), and detective quantum efficiency (DQE) that are widely used to characterize detector performance in radiographic imaging and would be ideal for QA purposes. However, due to the difficulty of performing conventional MTF measurements, they have not been used for routine clinical QA. The authors present a simple and quick QA methodology based on obtaining the MTF, NPS, and DQE of a megavoltage imager by imaging standard open fields and a bar-pattern QA phantom containing 2 mm thick tungsten line-pair bar resolution targets. Our bar-pattern based MTF measurement features a novel zero-frequency normalization scheme that eliminates normalization errors typically associated with traditional bar-pattern measurements at megavoltage x-ray energies. The bar-pattern QA phantom and open-field images are used in conjunction with an automated image analysis algorithm that quickly computes the MTF, NPS, and DQE of an EPID system. Our approach combines the fundamental advantages of

  11. Fluid-structure interactions of skeleton-reinforced fins: performance analysis of a paired fin in lift-based propulsion.

    PubMed

    Shoele, Kourosh; Zhu, Qiang

    2009-08-01

    We investigate the thrust generation capacity of a thin foil consisting of a membrane strengthened by embedded rays that is geometrically, structurally and kinematically similar to pectoral fins of bony fishes during lift-based labriform locomotion. Our numerical model includes a fully nonlinear Euler-Bernoulli beam model of the skeleton and a boundary-element model of the surrounding flow field. The fin undergoes a dorso-ventral flapping activated by rotations of the rays. Both the trailing edge vortices (TEV) and the leading edge vortices (LEV) are accounted for and modeled as shear layers. The thrust generation and propulsion efficiency are examined and documented. Our results show that synchronization of rays is pivotal to the performance of the system. A primary factor that determines the performance of the fin is phase lags between the rays, which create variations of the effective angle of attack at the leading edge as well as shape changes throughout the fin surface. Structural flexibility of the rays leads to passive deformations of the fin, which can increase the thrust generation and the propulsion efficiency. PMID:19648413

  12. An Intriguing Correlation Based on the Superimposition of Residue Pairs with Inhibitors that Target Protein-Protein Interfaces

    PubMed Central

    Nakadai, Masakazu; Tomida, Shuta; Sekimizu, Kazuhisa

    2016-01-01

    Druggable sites on protein-protein interfaces are difficult to predict. To survey inhibitor-binding sites onto which residues are superimposed at protein-protein interfaces, we analyzed publicly available information for 39 inhibitors that target the protein-protein interfaces of 8 drug targets. By focusing on the differences between residues that were superimposed with inhibitors and non-superimposed residues, we observed clear differences in the distances and changes in the solvent-accessible surface areas (∆SASA). Based on the observation that two or more residues were superimposed onto inhibitors in 37 (95%) of 39 protein-inhibitor complexes, we focused on the two-residue relationships. Application of a cross-validation procedure confirmed a linear negative correlation between the absolute value of the dihedral angle and the sum of the ∆SASAs of the residues. Finally, we applied the regression equation of this correlation to four inhibitors that bind to new sites not bound by the 39 inhibitors as well as additional inhibitors of different targets. Our results shed light on the two-residue correlation between the absolute value of the dihedral angle and the sum of the ∆SASA, which may be a useful relationship for identifying the key two-residues as potential targets of protein-protein interfaces. PMID:26730437

  13. The importance of inter- and intramolecular base pairing for translation reinitiation on a eukaryotic bicistronic mRNA.

    PubMed

    Luttermann, Christine; Meyers, Gregor

    2009-02-01

    Calicivirus structure proteins are expressed from a subgenomic mRNA with two overlapping cistrons. The first ORF of this RNA codes for the viral major capsid protein VP1, and the second for the minor capsid protein VP2. Translation of VP2 is mediated by a termination/reinitiation mechanism, which depends on an upstream sequence element of approximately 70 nucleotides denoted "termination upstream ribosomal binding site" (TURBS). Two short sequence motifs within the TURBS were found to be essential for reinitiation. By a whole set of single site mutations and reciprocal base exchanges we demonstrate here for the first time conclusive evidence for the necessity of mRNA/18S rRNA hybridization for translation reinitiation in an eukaryotic system. Moreover, we show that motif 2 exhibits intramolecular hybridization with a complementary region upstream of motif 1, thus forming a secondary structure that positions post-termination ribosomes in an optimal distance to the VP2 start codon. Analysis of the essential elements of the TURBS led to a better understanding of the requirements for translation termination/reinitiation in eukaryotes.

  14. MINARETS WILDERNESS AND ADJACENT AREAS, CALIFORNIA.

    USGS Publications Warehouse

    Huber, N. King; Thurber, Horace K.

    1984-01-01

    A mineral survey of the Minarets Wilderness and adjacent areas in the central Sierra Nevada, California was conducted. The results of the survey indicate that the study area has a substantiated resource potential for small deposits of copper, silver, zinc, lead, and iron, and a probable mineral-resource potential for molybdenum. No energy-resource potential was identified in the study.

  15. 46 CFR 148.445 - Adjacent spaces.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) DANGEROUS CARGOES CARRIAGE OF BULK SOLID MATERIALS... transporting a material that Table 148.10 of this part associates with a reference to this section, the following requirements must be met: (a) Each space adjacent to a cargo hold must be ventilated by...

  16. 46 CFR 148.445 - Adjacent spaces.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) DANGEROUS CARGOES CARRIAGE OF BULK SOLID MATERIALS... transporting a material that Table 148.10 of this part associates with a reference to this section, the following requirements must be met: (a) Each space adjacent to a cargo hold must be ventilated by...

  17. 46 CFR 148.445 - Adjacent spaces.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) DANGEROUS CARGOES CARRIAGE OF BULK SOLID MATERIALS... transporting a material that Table 148.10 of this part associates with a reference to this section, the following requirements must be met: (a) Each space adjacent to a cargo hold must be ventilated by...

  18. 46 CFR 148.445 - Adjacent spaces.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) DANGEROUS CARGOES CARRIAGE OF BULK SOLID MATERIALS... transporting a material that Table 148.10 of this part associates with a reference to this section, the following requirements must be met: (a) Each space adjacent to a cargo hold must be ventilated by...

  19. Conference room 211, adjacent to commander's quarters, with vault door ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Conference room 211, adjacent to commander's quarters, with vault door at right. Projection area at center is equipped with automatic security drapes. Projection room uses a 45 degree mirror to reflect the image onto the frosted glass screen. Door on far left leads to display area senior battle staff viewing bridge, and the commander's quarters - March Air Force Base, Strategic Air Command, Combat Operations Center, 5220 Riverside Drive, Moreno Valley, Riverside County, CA

  20. Pair contact process with diffusion of pairs

    NASA Astrophysics Data System (ADS)

    Santos, F. L.; Dickman, Ronald; Fulco, U. L.

    2011-03-01

    The pair contact process (PCP) is a nonequilibrium stochastic model which, like the basic contact process (CP), exhibits a phase transition to an absorbing state. The two models belong to the directed percolation (DP) universality class, despite the fact that the PCP possesses infinitely many absorbing configurations whereas the CP has but one. The critical behavior of the PCP with hopping by particles (PCPD) is as yet unclear. Here we study a version of the PCP in which nearest-neighbor particle pairs can hop but individual particles cannot. Using quasistationary simulations for three values of the diffusion probability (D = 0.1, 0.5 and 0.9), we find convincing evidence of DP-like critical behavior.

  1. Cooper Pairs in Insulators?!

    SciTech Connect

    James Valles

    2008-07-23

    Nearly 50 years elapsed between the discovery of superconductivity and the emergence of the microscopic theory describing this zero resistance state. The explanation required a novel phase of matter in which conduction electrons joined in weakly bound pairs and condensed with other pairs into a single quantum state. Surprisingly, this Cooper pair formation has also been invoked to account for recently uncovered high-resistance or insulating phases of matter. To address this possibility, we have used nanotechnology to create an insulating system that we can probe directly for Cooper pairs. I will present the evidence that Cooper pairs exist and dominate the electrical transport in these insulators and I will discuss how these findings provide new insight into superconductor to insulator quantum phase transitions. 

  2. Critical Schwinger Pair Production.

    PubMed

    Gies, Holger; Torgrimsson, Greger

    2016-03-01

    We investigate Schwinger pair production in spatially inhomogeneous electric backgrounds. A critical point for the onset of pair production can be approached by fields that marginally provide sufficient electrostatic energy for an off-shell long-range electron-positron fluctuation to become a real pair. Close to this critical point, we observe features of universality which are analogous to continuous phase transitions in critical phenomena with the pair-production rate serving as an order parameter: electric backgrounds can be subdivided into universality classes and the onset of pair production exhibits characteristic scaling laws. An appropriate design of the electric background field can interpolate between power-law scaling, essential Berezinskii-Kosterlitz-Thouless-type scaling, and a power-law scaling with log corrections. The corresponding critical exponents only depend on the large-scale features of the electric background, whereas the microscopic details of the background play the role of irrelevant perturbations not affecting criticality. PMID:26991162

  3. Cooper Pairs in Insulators?!

    ScienceCinema

    James Valles

    2016-07-12

    Nearly 50 years elapsed between the discovery of superconductivity and the emergence of the microscopic theory describing this zero resistance state. The explanation required a novel phase of matter in which conduction electrons joined in weakly bound pairs and condensed with other pairs into a single quantum state. Surprisingly, this Cooper pair formation has also been invoked to account for recently uncovered high-resistance or insulating phases of matter. To address this possibility, we have used nanotechnology to create an insulating system that we can probe directly for Cooper pairs. I will present the evidence that Cooper pairs exist and dominate the electrical transport in these insulators and I will discuss how these findings provide new insight into superconductor to insulator quantum phase transitions. 

  4. Facile one-pot preparation and functionalization of luminescent chitosan-poly(methacrylic acid) microspheres based on polymer monomer pairs

    NASA Astrophysics Data System (ADS)

    Guo, Jia; Wang, Changchun; Mao, Weiyong; Yang, Wuli; Liu, Changjia; Chen, Jiyao

    2008-08-01

    In this paper, we present a facile and robust approach to synthesize multifunctional organic/inorganic composite microspheres with chitosan-poly(methacrylic acid) (CS-PMAA) shells and cadmium tellurium/iron oxide nanoparticle cores. Due to the strong electrostatic interaction between the negatively charged nanoparticles and the protonated CS polymers, the CS/nanoparticle complexes were utilized as templates for the subsequent polymerization of methacrylic acid. The resulting composite microspheres with luminescence and magnetic properties have regular morphologies and narrow size distributions. In contrast to previous reports, this route was based on a one-pot strategy without the aid of surfactants, organic solvent, or polymerizable ligands in aqueous solution. The encapsulated CdTe semiconductor nanocrystals inside the microspheres exhibited strong and stable photoluminescence properties in the pH range 5.0-11.0. When the pH was adjusted below 4, the photoluminescence decreased sharply and even quenched completely. However, the weakened fluorescence emission could be recovered to some degree upon an increase of pH above 5. Additionally, when both Fe3O4 and CdTe nanoparticles were encapsulated within CS-PMAA microspheres, the magnetic content of the microspheres could be efficiently controlled by tuning the feeding molar ratio of MAA monomers and glucosamine units of CS. From the preliminary attempts, it was found that the multifunctional microspheres as imaging agents could improve the rate and extent of cellular uptake under short-term exposure to an applied magnetic field, and so exhibit a great potential as bioactive molecule carriers.

  5. Analytic energy derivatives for the calculation of the first-order molecular properties using the domain-based local pair-natural orbital coupled-cluster theory

    NASA Astrophysics Data System (ADS)

    Datta, Dipayan; Kossmann, Simone; Neese, Frank

    2016-09-01

    The domain-based local pair-natural orbital coupled-cluster (DLPNO-CC) theory has recently emerged as an efficient and powerful quantum-chemical method for the calculation of energies of molecules comprised of several hundred atoms. It has been demonstrated that the DLPNO-CC approach attains the accuracy of a standard canonical coupled-cluster calculation to about 99.9% of the basis set correlation energy while realizing linear scaling of the computational cost with respect to system size. This is achieved by combining (a) localized occupied orbitals, (b) large virtual orbital correlation domains spanned by the projected atomic orbitals (PAOs), and (c) compaction of the virtual space through a truncated pair natural orbital (PNO) basis. In this paper, we report on the implementation of an analytic scheme for the calculation of the first derivatives of the DLPNO-CC energy for basis set independent perturbations within the singles and doubles approximation (DLPNO-CCSD) for closed-shell molecules. Perturbation-independent one-particle density matrices have been implemented in order to account for the response of the CC wave function to the external perturbation. Orbital-relaxation effects due to external perturbation are not taken into account in the current implementation. We investigate in detail the dependence of the computed first-order electrical properties (e.g., dipole moment) on the three major truncation parameters used in a DLPNO-CC calculation, namely, the natural orbital occupation number cutoff used for the construction of the PNOs, the weak electron-pair cutoff, and the domain size cutoff. No additional truncation parameter has been introduced for property calculation. We present benchmark calculations on dipole moments for a set of 10 molecules consisting of 20-40 atoms. We demonstrate that 98%-99% accuracy relative to the canonical CCSD results can be consistently achieved in these calculations. However, this comes with the price of tightening the

  6. Investigation of quantum phase transitions in the spdf interacting boson model based on dual algebraic structures for the four-level pairing model

    NASA Astrophysics Data System (ADS)

    Jafarizadeh, M. A.; Jalili Majarshin, A.; Fouladi, N.; Ghapanvari, M.

    2016-09-01

    The building blocks of the interacting boson model (IBM) are associated with both s and d bosons for positive parity states. An extension of sd-IBM along these models to spdf-IBM can provide the appropriate framework to describe negative parity states. In this paper, a solvable extended transitional Hamiltonian based on the affine \\widehat{{SU}(1,1)} Lie algebra is proposed to describe low lying positive and negative parity states between the spherical and deformed gamma-unstable shape. Quantum phase transitions (QPTs) are investigated based on dual algebraic structures for the four-level pairing model. Numerical extraction to low-lying energy levels and transition rates within the control parameters of this evaluated Hamiltonian are presented for various N values. By reproducing the experimental results, the method based on the signatures of the phase transition, such as the expectation value of the boson number operators in the lowest excited states, are used to provide a better description of Ru isotopes in this transitional region.

  7. Base-pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium.

    PubMed

    Vasumathi, V; Daniel, M

    2009-12-01

    The protein-DNA interaction dynamics is studied by modeling the DNA bases as classical spins in a coupled spin system, which are bosonized and coupled to thermal phonons and longitudinal motion of the protein molecule in the nonviscous limit. The nonlinear dynamics of this protein-DNA complex molecular system is governed by the completely integrable nonlinear Schrödinger (NLS) equation which admits N -soliton solutions. The soliton excitations of the DNA bases in the two strands make localized base-pair opening and travel along the DNA chain in the form of a bubble. This may characterize the bubble generated during the transcription process, when an RNA polymerase binds to a promoter site in the DNA double helical chain. When the protein-DNA molecular system interacts with the surrounding viscous solvating water medium, the dynamics is governed by a perturbed NLS equation. This equation is solved using a multiple scale perturbation analysis, by treating the viscous effect as a weak perturbation, and the results show that the viscosity of the solvent medium damps out the soliton as time progresses. PMID:20365187

  8. Catalytic CO2 activation assisted by rhenium hydride/B(C6F5)3 frustrated Lewis pairs--metal hydrides functioning as FLP bases.

    PubMed

    Jiang, Yanfeng; Blacque, Olivier; Fox, Thomas; Berke, Heinz

    2013-05-22

    Reaction of 1 with B(C6F5)3 under 1 bar of CO2 led to the instantaneous formation of the frustrated Lewis pair (FLP)-type species [ReHBr(NO)(PR3)2(η(2)-O═C═O-B(C6F5)3)] (2, R = iPr a, Cy b) possessing two cis-phosphines and O(CO2)-coordinated B(C6F5)3 groups as verified by NMR spectroscopy and supported by DFT calculations. The attachment of B(C6F5)3 in 2a,b establishes cooperative CO2 activation via the Re-H/B(C6F5)3 Lewis pair, with the Re-H bond playing the role of a Lewis base. The Re(I) η(1)-formato dimer [{Re(μ-Br)(NO)(η(1)-OCH═O-B(C6F5)3)(PiPr3)2}2] (3a) was generated from 2a and represents the first example of a stable rhenium complex bearing two cis-aligned, sterically bulky PiPr3 ligands. Reaction of 3a with H2 cleaved the μ-Br bridges, producing the stable and fully characterized formato dihydrogen complex [ReBrH2(NO)(η(1)-OCH═O-B(C6F5)3)(PiPr3)2] (4a) bearing trans-phosphines. Stoichiometric CO2 reduction of 4a with Et3SiH led to heterolytic splitting of H2 along with formation of bis(triethylsilyl)acetal ((Et3SiO)2CH2, 7). Catalytic reduction of CO2 with Et3SiH was also accomplished with the catalysts 1a,b/B(C6F5)3, 3a, and 4a, showing turnover frequencies (TOFs) between 4 and 9 h(-1). The stoichiometric reaction of 4a with the sterically hindered base 2,2,6,6-tetramethylpiperidine (TMP) furnished H2 ligand deprotonation. Hydrogenations of CO2 using 1a,b/B(C6F5)3, 3a, and 4a as catalysts gave in the presence of TMP TOFs of up to 7.5 h(-1), producing [TMPH][formate] (11). The influence of various bases (R2NH, R = iPr, Cy, SiMe3, 2,4,6-tri-tert-butylpyridine, NEt3, PtBu3) was studied in greater detail, pointing to two crucial factors of the CO2 hydrogenations: the steric bulk and the basicity of the base.

  9. Lax pairs for deformed Minkowski spacetimes

    NASA Astrophysics Data System (ADS)

    Kyono, Hideki; Sakamoto, Jun-ichi; Yoshida, Kentaroh

    2016-01-01

    We proceed to study Yang-Baxter deformations of 4D Minkowski spacetime based on a conformal embedding. We first revisit a Melvin background and argue a Lax pair by adopting a simple replacement law invented in 1509.00173. This argument enables us to deduce a general expression of Lax pair. Then the anticipated Lax pair is shown to work for arbitrary classical r-matrices with Poincaré generators. As other examples, we present Lax pairs for pp-wave backgrounds, the Hashimoto-Sethi background, the Spradlin-Takayanagi-Volovich background.

  10. Stereo Pair, Pasadena, California

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This stereoscopic image pair is a perspective view that shows the western part of the city of Pasadena, California, looking north toward the San Gabriel Mountains. Portions of the cities of Altadena and La Canada Flintridge are also shown. The cluster of large buildings left of center, at the base of the mountains, is the Jet Propulsion Laboratory. This image shows the power of combining data from different sources to create planning tools to study problems that affect large urban areas. In addition to the well-known earthquake hazards, Southern California is affected by a natural cycle of fire and mudflows. Data shown in this image can be used to predict both how wildfires spread over the terrain and how mudflows are channeled down the canyons.

    The image was created from three datasets: the Shuttle Radar Topography Mission (SRTM) supplied the elevation, U. S. Geological Survey digital aerial photography provided the image detail, and the Landsat Thematic Mapper provided the color. The United States Geological Survey's Earth Resources Observations Systems (EROS) Data Center, Sioux Falls, South Dakota, provided the Landsat data and the aerial photography. The image can be viewed in 3-D by viewing the left image with the right eye and the right image with the left eye (cross-eyed viewing), or by downloading and printing the image pair, and viewing them with a stereoscope.

    The Shuttle Radar Topography Mission (SRTM), launched on February 11, 2000, used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. The mission was designed to collect three-dimensional measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter-long (200-foot) mast, an additional C-band imaging antenna and improved tracking and navigation devices. The mission is a cooperative project between the National Aeronautics and Space Administration

  11. Effect of speckle on lidar pulse-pair ratio statistics.

    PubMed

    Mackerrow, E P; Schmitt, M J; Thompson, D C

    1997-11-20

    The ratio of temporally adjacent lidar pulse returns is commonly used in differential absorption lidar (DIAL) to reduce correlated noise. These pulses typically are generated at different wavelengths with the assumption that the dominant noise is common to both. This is not the case when the mean number of laser speckle integrated per pulse by the lidar receiver is small (namely, less than 10 speckles at each wavelength). In this case a large increase in the standard deviation of the ratio data results. We demonstrate this effect both theoretically and experimentally. The theoretical value for the expected standard deviation of the pulse-pair ratio data compares well with the measured values that used a dual CO(2) laser-based lidar with a hard target. Pulse averaging statistics of the pulse-pair data obey the expected varsigma(1)/ radicalN reduction in the standard deviation, varsigma(N), for N-pulse averages. We consider the ratio before average, average before ratio, and log of the ratio before average methods for noise reduction in the lidar equation. The implications of our results are discussed in the context of dual-laser versus single-laser lidar configurations.

  12. Adjacent Segment Pathology after Lumbar Spinal Fusion.

    PubMed

    Lee, Jae Chul; Choi, Sung-Woo

    2015-10-01

    One of the major clinical issues encountered after lumbar spinal fusion is the development of adjacent segment pathology (ASP) caused by increased mechanical stress at adjacent segments, and resulting in various radiographic changes and clinical symptoms. This condition may require surgical intervention. The incidence of ASP varies with both the definition and methodology adopted in individual studies; various risk factors for this condition have been identified, although a significant controversy still exists regarding their significance. Motion-preserving devices have been developed, and some studies have shown their efficacy of preventing ASP. Surgeons should be aware of the risk factors of ASP when planning a surgery, and accordingly counsel their patients preoperatively. PMID:26435804

  13. Adjacent Segment Pathology after Lumbar Spinal Fusion

    PubMed Central

    Lee, Jae Chul

    2015-01-01

    One of the major clinical issues encountered after lumbar spinal fusion is the development of adjacent segment pathology (ASP) caused by increased mechanical stress at adjacent segments, and resulting in various radiographic changes and clinical symptoms. This condition may require surgical intervention. The incidence of ASP varies with both the definition and methodology adopted in individual studies; various risk factors for this condition have been identified, although a significant controversy still exists regarding their significance. Motion-preserving devices have been developed, and some studies have shown their efficacy of preventing ASP. Surgeons should be aware of the risk factors of ASP when planning a surgery, and accordingly counsel their patients preoperatively. PMID:26435804

  14. Paired Straight Hearth Furnace

    SciTech Connect

    2009-04-01

    This factsheet describes a research project whose goals are to design, develop, and evaluate the scalability and commercial feasibility of the PSH Paired Straight Hearth Furnace alternative ironmaking process.

  15. Adaptive Pairing Reversible Watermarking.

    PubMed

    Dragoi, Ioan-Catalin; Coltuc, Dinu

    2016-05-01

    This letter revisits the pairwise reversible watermarking scheme of Ou et al., 2013. An adaptive pixel pairing that considers only pixels with similar prediction errors is introduced. This adaptive approach provides an increased number of pixel pairs where both pixels are embedded and decreases the number of shifted pixels. The adaptive pairwise reversible watermarking outperforms the state-of-the-art low embedding bit-rate schemes proposed so far.

  16. Konnector v2.0: pseudo-long reads from paired-end sequencing data

    PubMed Central

    2015-01-01

    Background Reading the nucleotides from two ends of a DNA fragment is called paired-end tag (PET) sequencing. When the fragment length is longer than the combined read length, there remains a gap of unsequenced nucleotides between read pairs. If the target in such experiments is sequenced at a level to provide redundant coverage, it may be possible to bridge these gaps using bioinformatics methods. Konnector is a local de novo assembly tool that addresses this problem. Here we report on version 2.0 of our tool. Results Konnector uses a probabilistic and memory-efficient data structure called Bloom filter to represent a k-mer spectrum - all possible sequences of length k in an input file, such as the collection of reads in a PET sequencing experiment. It performs look-ups to this data structure to construct an implicit de Bruijn graph, which describes (k-1) base pair overlaps between adjacent k-mers. It traverses this graph to bridge the gap between a given pair of flanking sequences. Conclusions Here we report the performance of Konnector v2.0 on simulated and experimental datasets, and compare it against other tools with similar functionality. We note that, representing k-mers with 1.5 bytes of memory on average, Konnector can scale to very large genomes. With our parallel implementation, it can also process over a billion bases on commodity hardware. PMID:26399504

  17. Adjacent Segment Pathology after Anterior Cervical Fusion.

    PubMed

    Chung, Jae Yoon; Park, Jong-Beom; Seo, Hyoung-Yeon; Kim, Sung Kyu

    2016-06-01

    Anterior cervical fusion has become a standard of care for numerous pathologic conditions of the cervical spine. However, subsequent development of clinically significant disc disease at levels adjacent to fused discs is a serious long-term complication of this procedure. As more patients live longer after surgery, it is foreseeable that adjacent segment pathology (ASP) will develop in increasing numbers of patients. Also, ASP has been studied more intensively with the recent popularity of motion preservation technologies like total disc arthroplasty. The true nature and scope of ASP remains poorly understood. The etiology of ASP is most likely multifactorial. Various factors including altered biomechanical stresses, surgical disruption of soft tissue and the natural history of cervical disc disease contribute to the development of ASP. General factors associated with disc degeneration including gender, age, smoking and sports may play a role in the development of ASP. Postoperative sagittal alignment and type of surgery are also considered potential causes of ASP. Therefore, a spine surgeon must be particularly careful to avoid unnecessary disruption of the musculoligamentous structures, reduced risk of direct injury to the disc during dissection and maintain a safe margin between the plate edge and adjacent vertebrae during anterior cervical fusion.

  18. Adjacent Segment Pathology after Anterior Cervical Fusion

    PubMed Central

    Chung, Jae Yoon; Park, Jong-Beom; Seo, Hyoung-Yeon

    2016-01-01

    Anterior cervical fusion has become a standard of care for numerous pathologic conditions of the cervical spine. However, subsequent development of clinically significant disc disease at levels adjacent to fused discs is a serious long-term complication of this procedure. As more patients live longer after surgery, it is foreseeable that adjacent segment pathology (ASP) will develop in increasing numbers of patients. Also, ASP has been studied more intensively with the recent popularity of motion preservation technologies like total disc arthroplasty. The true nature and scope of ASP remains poorly understood. The etiology of ASP is most likely multifactorial. Various factors including altered biomechanical stresses, surgical disruption of soft tissue and the natural history of cervical disc disease contribute to the development of ASP. General factors associated with disc degeneration including gender, age, smoking and sports may play a role in the development of ASP. Postoperative sagittal alignment and type of surgery are also considered potential causes of ASP. Therefore, a spine surgeon must be particularly careful to avoid unnecessary disruption of the musculoligamentous structures, reduced risk of direct injury to the disc during dissection and maintain a safe margin between the plate edge and adjacent vertebrae during anterior cervical fusion. PMID:27340541

  19. Resonantly paired fermionic superfluids

    NASA Astrophysics Data System (ADS)

    Gurarie, V.; Radzihovsky, L.

    2007-01-01

    We present a theory of a degenerate atomic Fermi gas, interacting through a narrow Feshbach resonance, whose position and therefore strength can be tuned experimentally, as demonstrated recently in ultracold trapped atomic gases. The distinguishing feature of the theory is that its accuracy is controlled by a dimensionless parameter proportional to the ratio of the width of the resonance to Fermi energy. The theory is therefore quantitatively accurate for a narrow Feshbach resonance. In the case of a narrow s-wave resonance, our analysis leads to a quantitative description of the crossover between a weakly paired BCS superconductor of overlapping Cooper pairs and a strongly paired molecular Bose-Einstein condensate of diatomic molecules. In the case of pairing via a p-wave resonance, that we show is always narrow for a sufficiently low density, we predict a detuning-temperature phase diagram, that in the course of a BCS-BEC crossover can exhibit a host of thermodynamically distinct phases separated by quantum and classical phase transitions. For an intermediate strength of the dipolar anisotropy, the system exhibits a px + i py paired superfluidity that undergoes a topological phase transition between a weakly coupled gapless ground state at large positive detuning and a strongly paired fully gapped molecular superfluid for a negative detuning. In two dimensions the former state is characterized by a Pfaffian ground state exhibiting topological order and non-Abelian vortex excitations familiar from fractional quantum Hall systems.

  20. Cooper Pair Insulators

    NASA Astrophysics Data System (ADS)

    Valles, James

    One of the recent advances in the field of the Superconductor to Insulator Transition (SIT) has been the discovery and characterization of the Cooper Pair Insulator phase. This bosonic insulator, which consists of localized Cooper pairs, exhibits activated transport and a giant magneto-resistance peak. These features differ markedly from the weakly localized transport that emerges as pairs break at a ``fermionic'' SIT. I will describe how our experiments on films nano-patterned with a nearly triangular array of holes have enabled us to 1) distinguish bosonic insulators from fermionic insulators, 2) show that Cooper pairs, rather than quasi-particles dominate the transport in the Cooper Pair insulator phase, 3) demonstrate that very weak, sub nano-meter thickness inhomogeneities control whether a bosonic or fermionic insulator forms at an SIT and 4) reveal that Cooper pairs disintegrate rather than becoming more tightly bound deep in the localized phase. We have also developed a method, using a magnetic field, to tune flux disorder reversibly in these films. I will present our latest results on the influence of magnetic flux disorder and random gauge fields on phenomena near bosonic SITs. This work was performed in collaboration with M. D. Stewart, Jr., Hung Q. Nguyen, Shawna M. Hollen, Jimmy Joy, Xue Zhang, Gustavo Fernandez, Jeffrey Shainline and Jimmy Xu. It was supported by NSF Grants DMR 1307290 and DMR-0907357.

  1. Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA.

    PubMed

    Fuentes-Cabrera, Miguel; Sumpter, Bobby G; Sponer, Judit E; Sponer, Jirí; Petit, Leon; Wells, Jack C

    2007-02-01

    M-DNA is a type of metalated DNA that forms at high pH and in the presence of Zn, Ni, and Co, with the metals placed in between each base pair, as in G-Zn-C. Experiments have found that M-DNA could be a promising candidate for a variety of nanotechnological applications, as it is speculated that the metal d-states enhance the conductivity, but controversy still clouds these findings. In this paper, we carry out a comprehensive ab initio study of eight G-Zn-C models in the gas phase to help discern the structure and electronic properties of Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties that correlate with Zn-DNA having a metallic-like conductivity. Out of all the studied models, there is only one which preserves its planarity upon full geometry optimization. Nevertheless, starting from this model, one can deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast to what has been proposed experimentally. Among the nonplanar models, there is one that requires less than 8 kcal/mol to flatten (both in gas and solvent conditions), and we propose that it is a plausible model for building an antiparallel duplex. In this duplex, the imino proton would be replaced by Zn, in accordance with experimental models. Neither planar nor nonplanar models have electronic properties that correlate with Zn-DNA having a metallic-like conductivity due to Zn d-states. To understand whether density functional theory (DFT) can describe appropriately the electronic properties of M-DNAs, we have investigated the electronic properties of G-Co-C base pairs. We have found that when self-interaction corrections (SIC) are not included the HOMO state contains Co d-levels, whereas these levels are moved below the HOMO state when SIC are considered. This result indicates that caution should be exercised when studying the electronic properties of M-DNAs with functionals that do not account for strong

  2. Conflict of mitochondrial phylogeny and morphology-based classification in a pair of freshwater gastropods (Caenogastropoda, Truncatelloidea, Tateidae) from New Caledonia

    PubMed Central

    Becker, Marlen; Zielske, Susan; Haase, Martin

    2016-01-01

    Abstract Morphological classification and mitochondrial phylogeny of a pair of morphologically defined species of New Caledonian freshwater gastropods, Hemistomia cockerelli and Hemistomia fabrorum, were incongruent. We asked whether these two nominal species can be unambiguously distinguished based on shell morphology or whether the taxonomic discrepancy inferred from these character types was reflected in the variation of shell morphology. Our investigations were based on phylogenetic analyses of a fragment of the mitochondrial cytochrome c oxidase subunit I, geometric morphometric analyses as well as micro computer tomography. The species presorted to morphospecies by eye overlapped in shell shape. However, statistically, all shells were correctly assigned, but not all of them significantly. Qualitatively, both nominal species can be unambiguously distinguished by the presence/absence of a prominent denticle within the shell. In the phylogenetic analyses, individuals from three populations clustered with the “wrong” morphospecies. In the absence of data from multiple loci, it was assumed for the single specimen from one of these populations that its misplacement was due to a recent hybridization event, based on its very shallow position in the tree. For the other two cases of misplacement neither introgression nor incomplete lineage sorting could be ruled out. Further investigations have to show whether the morphological overlap has a genetic basis or is due to phenotypic plasticity. In conclusion, despite their partly unresolved relationships Hemistomia cockerelli and Hemistomia fabrorum may be considered sister species, which are reliably diagnosable by the presence or absence of the denticle, but have not yet fully differentiated in all character complexes investigated. PMID:27551195

  3. The ambiguous base-pairing and high substrate efficiency of T-705 (Favipiravir) Ribofuranosyl 5'-triphosphate towards influenza A virus polymerase.

    PubMed

    Jin, Zhinan; Smith, Lucas K; Rajwanshi, Vivek K; Kim, Baek; Deval, Jerome

    2013-01-01

    T-705 (Favipiravir) is a broad-spectrum antiviral molecule currently in late stage clinical development for the treatment of influenza virus infection. Although it is believed that T-705 potency is mediated by its ribofuranosyl triphosphate (T-705 RTP) metabolite that could be mutagenic, the exact molecular interaction with the polymerase of influenza A virus (IAVpol) has not been elucidated. Here, we developed a biochemical assay to measure the kinetics of nucleotide incorporation by IAVpol in the elongation mode. In this assay, T-705 RTP was recognized by IAVpol as an efficient substrate for incorporation to the RNA both as a guanosine and an adenosine analog. Compared to natural GTP and ATP, the discrimination of T-705 RTP was about 19- and 30-fold, respectively. Although the single incorporation of the ribonucleotide monophosphate form of T-705 did not efficiently block RNA synthesis, two consecutive incorporation events prevented further primer extension. In comparison, 3'-deoxy GTP caused immediate chain termination but was incorporated less efficiently by the enzyme, with a discrimination of 4,900-fold relative to natural GTP. Collectively, these results provide the first detailed biochemical characterization to evaluate the substrate efficiency and the inhibition potency of nucleotide analogs against influenza virus polymerase. The combination of ambiguous base-pairing with low discrimination of T-705 RTP provides a mechanistic basis for the in vitro mutagenic effect of T-705 towards influenza virus.

  4. In-Phase Assembly of Slim DNA Lattices with Small Circular DNA Motifs via Short Connections of 11 and 16 Base Pairs.

    PubMed

    Wang, Meng; Guo, Xin; Jiang, Chuan; Wang, Xuemei; Xiao, Shou-Jun

    2016-06-16

    Two kinds of stable motif were constructed: SAE (semi-crossover, antiparallel, even half-turns) tile from one small circular DNA molecule (42 or 64 nt) and two linear oligonucleotides; and DAE (double-crossover, antiparallel, even half-turns) tile from one small circular DNA molecule (42 or 64 nt) and four linear oligonucleotides. With the SAE tiles, in-phase assembly of SAE-E (SAE tiles with even half-turns as connections (-E)) with the shortest -E of 11 base pairs (bp) generated homogeneous nanotubes with an average length of over 14 μm and a diameter of 16-20 nm; with the DAE tiles, in-phase assembly of DAE-O (DAE tiles with odd half-turns as connections (-O)) with the shortest -O of 16 bp produced slim monolayer nanoyarns (25-30 nm wide), nanoscarfs (100-300 nm wide), and nanoribbons (∼100 nm wide). Interestingly, a phenomenon we term "knitting nanoyarns" into nanoscarfs was observed. Finally a curvature mechanism according to the ring rotation directions is suggested to explain the formation of nanotubes, wavy nanoyarns, nanoscarfs, and nanoribbons.

  5. The Ambiguous Base-Pairing and High Substrate Efficiency of T-705 (Favipiravir) Ribofuranosyl 5′-Triphosphate towards Influenza A Virus Polymerase

    PubMed Central

    Jin, Zhinan; Smith, Lucas K.; Rajwanshi, Vivek K.; Kim, Baek; Deval, Jerome

    2013-01-01

    T-705 (Favipiravir) is a broad-spectrum antiviral molecule currently in late stage clinical development for the treatment of influenza virus infection. Although it is believed that T-705 potency is mediated by its ribofuranosyl triphosphate (T-705 RTP) metabolite that could be mutagenic, the exact molecular interaction with the polymerase of influenza A virus (IAVpol) has not been elucidated. Here, we developed a biochemical assay to measure the kinetics of nucleotide incorporation by IAVpol in the elongation mode. In this assay, T-705 RTP was recognized by IAVpol as an efficient substrate for incorporation to the RNA both as a guanosine and an adenosine analog. Compared to natural GTP and ATP, the discrimination of T-705 RTP was about 19- and 30-fold, respectively. Although the single incorporation of the ribonucleotide monophosphate form of T-705 did not efficiently block RNA synthesis, two consecutive incorporation events prevented further primer extension. In comparison, 3′-deoxy GTP caused immediate chain termination but was incorporated less efficiently by the enzyme, with a discrimination of 4,900-fold relative to natural GTP. Collectively, these results provide the first detailed biochemical characterization to evaluate the substrate efficiency and the inhibition potency of nucleotide analogs against influenza virus polymerase. The combination of ambiguous base-pairing with low discrimination of T-705 RTP provides a mechanistic basis for the in vitro mutagenic effect of T-705 towards influenza virus. PMID:23874596

  6. Alteration of intersubunit acid–base pair interactions at the quasi-threefold axis of symmetry of Cucumber mosaic virus disrupts aphid vector transmission

    SciTech Connect

    Bricault, Christine A.; Perry, Keith L.

    2013-06-05

    In the atomic model of Cucumber mosaic virus (CMV), six amino acid residues form stabilizing salt bridges between subunits of the asymmetric unit at the quasi-threefold axis of symmetry. To evaluate the effects of these positions on virion stability and aphid vector transmissibility, six charged amino acid residues were individually mutated to alanine. All of the six engineered viruses were viable and exhibited near wild type levels of virion stability in the presence of urea. Aphid vector transmissibility was nearly or completely eliminated in the case of four of the mutants; two mutants demonstrated intermediate aphid transmissibility. For the majority of the engineered mutants, second-site mutations were observed following aphid transmission and/or mechanical passaging, and one restored transmission rates to that of the wild type. CMV capsids tolerate disruption of acid–base pairing interactions at the quasi-threefold axis of symmetry, but these interactions are essential for maintaining aphid vector transmissibility. - Highlights: ► Amino acids between structural subunits of Cucumber mosaic virus affect vector transmission. ► Mutant structural stability was retained, while aphid vector transmissibility was disrupted. ► Spontaneous, second-site mutations restored aphid vector transmissibility.

  7. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq).

    PubMed

    Mahat, Dig Bijay; Kwak, Hojoong; Booth, Gregory T; Jonkers, Iris H; Danko, Charles G; Patel, Ravi K; Waters, Colin T; Munson, Katie; Core, Leighton J; Lis, John T

    2016-08-01

    We provide a protocol for precision nuclear run-on sequencing (PRO-seq) and its variant, PRO-cap, which map the location of active RNA polymerases (PRO-seq) or transcription start sites (TSSs) (PRO-cap) genome-wide at high resolution. The density of RNA polymerases at a particular genomic locus directly reflects the level of nascent transcription at that region. Nuclei are isolated from cells and, under nuclear run-on conditions, transcriptionally engaged RNA polymerases incorporate one or, at most, a few biotin-labeled nucleotide triphosphates (biotin-NTPs) into the 3' end of nascent RNA. The biotin-labeled nascent RNA is used to prepare sequencing libraries, which are sequenced from the 3' end to provide high-resolution positional information for the RNA polymerases. PRO-seq provides much higher sensitivity than ChIP-seq, and it generates a much larger fraction of usable sequence reads than ChIP-seq or NET-seq (native elongating transcript sequencing). Similarly to NET-seq, PRO-seq maps the RNA polymerase at up to base-pair resolution with strand specificity, but unlike NET-seq it does not require immunoprecipitation. With the protocol provided here, PRO-seq (or PRO-cap) libraries for high-throughput sequencing can be generated in 4-5 working days. The method has been applied to human, mouse, Drosophila melanogaster and Caenorhabditis elegans cells and, with slight modifications, to yeast. PMID:27442863

  8. Comparison of Predictive Immunohistochemical Marker Expression of Primary Breast Cancer and Paired Distant Metastasis using Surgical Material: A Practice-Based Study.

    PubMed

    Kulka, Janina; Székely, Borbála; Lukács, Lilla V; Kiss, Orsolya; Tőkés, Anna-Mária; Vincze, Eszter; Turányi, Eszter; Fillinger, János; Hanzély, Zoltán; Arató, Gabriella; Szendrői, Miklós; Győrffy, Balázs; Szász, A Marcell

    2016-04-01

    Parallel studies of primary breast carcinomas and corresponding distant metastases samples reveal considerable differences. Our aim was to highlight this issue from another perspective and provide further data based on 98 patient samples: 69 primary breast carcinoma and 85 distant metastases from bone, central nervous system (CNS) and lung (56 paired). Two independent series of immunohistochemical reactions with different antibodies for estrogen receptor (ER), progesterone receptor (PgR) and human epidermal growth factor receptor 2 (Her2), along with HER2 fluroscence in situ hybridization (FISH) were performed on tissue microarrays to classify breast carcinoma and distant metastases samples into Luminal A, Luminal B-proliferating, Luminal B-HER2+, HER2+ and triple negative (TNBC) surrogate breast cancer groups. Correlation and agreement between the two assessments of ER and PgR were fair-to-moderate, and almost perfect for HER2 and Ki67. There was 40% discordance concerning immunophenotype between breast carcinomas and distant metastases. Most common metastatic site of ER+ breast carcinoma was the skeletal system (59.2%), whereas that of TNBCs was the CNS (58.8%) and lungs (23.5%). Distant metastases in bones were mostly luminal (54.3%), in the CNS, Luminal B (53.2%), and in the lung, TNBC (37.5%). The change of drugable properties of primary breast cancers in the respective bone and CNS metastases suggests that characterization of the metastasis is necessary for appropriate treatment planning. PMID:27029768

  9. A FRET-based probe for epidermal growth factor receptor bound non-covalently to a pair of synthetic amphipathic helixes

    SciTech Connect

    Itoh, Reina E.; Kurokawa, Kazuo; Fujioka, Aki; Sharma, Alok; Mayer, Bruce J.; Matsuda, Michiyuki . E-mail: matsudam@biken.osaka-u.ac.jp

    2005-07-01

    Epidermal growth factor (EGF) receptor plays a pivotal role in a variety of cellular functions, such as proliferation, differentiation, and migration. To monitor the EGF receptor (EGFR) activity in living cells, we developed a probe for EGFR activity based on the principle of fluorescence resonance energy transfer (FRET). Previously, we developed a probe designated as Picchu (Phosphorylation indicator of the CrkII chimeric unit), which detects the tyrosine phosphorylation of the CrkII adaptor protein. We used a pair of synthetic amphipathic helixes, WinZipA2 and WinZipB1, to bind Picchu non-covalently to the carboxyl-terminus of the EGFR. Using this modified probe named Picchu-Z, the activity of EGFR was followed in EGF-stimulated Cos7 cells. We found that a high level of tyrosine phosphorylation of Picchu-Z probe remained after endocytosis until the point when the EGFR was translocated to the perinuclear region. These findings are in agreement with the previously reported 'signaling endosome' model. Furthermore, by pulse stimulation with EGF and by acute ablation of EGFR activity with AG1478, it was suggested that the phosphorylation of Picchu-Z probe, and probably the phosphorylation of EGFR also, underwent a rapid equilibrium ({tau} {sub 1/2} < 2 min) between the phosphorylated and dephosphorylated states in the presence of EGF.

  10. Comparison of Predictive Immunohistochemical Marker Expression of Primary Breast Cancer and Paired Distant Metastasis using Surgical Material: A Practice-Based Study.

    PubMed

    Kulka, Janina; Székely, Borbála; Lukács, Lilla V; Kiss, Orsolya; Tőkés, Anna-Mária; Vincze, Eszter; Turányi, Eszter; Fillinger, János; Hanzély, Zoltán; Arató, Gabriella; Szendrői, Miklós; Győrffy, Balázs; Szász, A Marcell

    2016-04-01

    Parallel studies of primary breast carcinomas and corresponding distant metastases samples reveal considerable differences. Our aim was to highlight this issue from another perspective and provide further data based on 98 patient samples: 69 primary breast carcinoma and 85 distant metastases from bone, central nervous system (CNS) and lung (56 paired). Two independent series of immunohistochemical reactions with different antibodies for estrogen receptor (ER), progesterone receptor (PgR) and human epidermal growth factor receptor 2 (Her2), along with HER2 fluroscence in situ hybridization (FISH) were performed on tissue microarrays to classify breast carcinoma and distant metastases samples into Luminal A, Luminal B-proliferating, Luminal B-HER2+, HER2+ and triple negative (TNBC) surrogate breast cancer groups. Correlation and agreement between the two assessments of ER and PgR were fair-to-moderate, and almost perfect for HER2 and Ki67. There was 40% discordance concerning immunophenotype between breast carcinomas and distant metastases. Most common metastatic site of ER+ breast carcinoma was the skeletal system (59.2%), whereas that of TNBCs was the CNS (58.8%) and lungs (23.5%). Distant metastases in bones were mostly luminal (54.3%), in the CNS, Luminal B (53.2%), and in the lung, TNBC (37.5%). The change of drugable properties of primary breast cancers in the respective bone and CNS metastases suggests that characterization of the metastasis is necessary for appropriate treatment planning.

  11. Multicomponent Molecular Puzzles for Photofunction Design: Emission Color Variation in Lewis Acid-Base Pair Crystals Coupled with Guest-to-Host Charge Transfer Excitation.

    PubMed

    Ono, Toshikazu; Sugimoto, Manabu; Hisaeda, Yoshio

    2015-08-01

    Simple yet ubiquitous multimolecular assembly systems with color-tunable emissions are realized by cooperative electron donor-acceptor interactions, such as the boron-nitrogen (B-N) dative bond as a Lewis acid-base pair and charge transfer (CT) interactions. These are ternary-component systems consisting of a naphthalenediimide derivative (NDI), tris(pentafluorophenyl)borane (TPFB), and aromatic molecules (guest) with an NDI:TPFB:guest ratio of 1:2:2. The crystal shows guest-dependent color-tunable emissions such as deep blue to orange when a guest molecule of benzene is replaced with other π-conjugated systems. A good correlation between the emission wavelength and ionization potential of the guest and electronic structure calculations indicated that the emission is due to the CT transition from the guest to the NDI. The present study suggests that a rational solution of multcomponent molecular puzzles would be useful for obtaining novel photofunctional solid-state systems. PMID:26211567

  12. Recognition by nonaromatic and stereochemical subunit-containing polyamides of the four Watson-Crick base pairs in the DNA minor groove.

    PubMed

    Zhang, Hong-Fei; Wu, Yan-Ling; Jiang, Shi-Kun; Wang, Pu; Sugiyama, Hiroshi; Chen, Xing-Lai; Zhang, Wen; Ji, Yan-Juan; Guo, Chuan-Xin

    2012-06-18

    In order to develop an optimal subunit as a T-recognition element in hairpin polyamides, 15 novel chirality-modified polyamides containing (R)-α,β-diaminopropionic acid ((R) β α-NH 2), (S)-α,β-diaminopropionic acid ((S) β α-NH 2), (1R,3S)-3-aminocyclopentanecarboxylic acid ((RS) Cp), (1S,3R)-3-amino-cyclopentanecarboxylic acid ((RS) Cp), (1R,3R)-3-aminocyclopentanecarboxylic acid ((RR) Cp) and (1S,3S)-3-amino-cyclopentanecarboxylic acid ((SS) Cp) residues were synthesized. Their binding characteristics to DNA sequences 5'-TGCNCAT-3'/3'-ACGN'GTA-5' (N⋅N'=A⋅T, T⋅A, G⋅C and C⋅G) were systemically studied by surface plasmon resonance (SPR) and molecular simulation (MSim) techniques. SPR showed that polyamide 4, AcIm-(S) β α-NH 2-ImPy-γ-ImPy-β-Py-βDp (β/(S) β α-NH 2 pair), bound to a DNA sequence containing a core binding site of 5'-TGCACAT-3' with a dissociation equilibrium constant (K(D) ) of 4.5×10(-8)  m. This was a tenfold improvement in specificity over 5'-TGCTCAT-3' (K(D) =4.5×10(-7)  M). MSim studies supported the SPR results. More importantly, for the first time, we found that chiral 3-aminocyclopentanecarboxylic acids in polyamides can be employed as base readers with only a small decrease in binding affinity to DNA. In particular, SPR showed that polyamide 9 ((RR) Cp/β pair) had a 15-fold binding preference for 5'-TGCTCAT-3' over 5'-TGCACAT-3'. A large difference in standard free energy change for A⋅T over T⋅A was determined (ΔΔG(o) =5.9 kJ mol(-1) ), as was a twofold decrease in interaction energy by MSim. Moreover, a 1:1 stoichiometry (9 to 5'-TGCTCAT-3'/3'-ACGAGTA-5') was shown by MSim to be optimal for the chiral five-membered cycle to fit the minor groove. Collectively, the study suggests that the (S)-α-amino-β-aminopropionic acid and (1R,3R)-3-aminocyclopentanecarboxylic acid can serve as a T-recognition element, and the stereochemistry and the nature of these subunits significantly influence

  13. Combinatorial DNA Damage Pairing Model Based on X-Ray-Induced Foci Predicts the Dose and LET Dependence of Cell Death in Human Breast Cells

    SciTech Connect

    Vadhavkar, Nikhil; Pham, Christopher; Georgescu, Walter; Deschamps, Thomas; Heuskin, Anne-Catherine; Tang, Jonathan; Costes, Sylvain V.

    2014-09-01

    are based on experimental RIF and are three times larger than the hypothetical LEM voxel used to fit survival curves. Our model is therefore an alternative to previous approaches that provides a testable biological mechanism (i.e., RIF). In addition, we propose that DSB pairing will help develop more accurate alternatives to the linear cancer risk model (LNT) currently used for regulating exposure to very low levels of ionizing radiation.

  14. A reference skeletal dosimetry model for an adult male radionuclide therapy patient based on three-dimensional imaging and paired-image radiation transport

    NASA Astrophysics Data System (ADS)

    Shah, Amish P.

    The need for improved patient-specificity of skeletal dose estimates is widely recognized in radionuclide therapy. Current clinical models for marrow dose are based on skeletal mass estimates from a variety of sources and linear chord-length distributions that do not account for particle escape into cortical bone. To predict marrow dose, these clinical models use a scheme that requires separate calculations of cumulated activity and radionuclide S values. Selection of an appropriate S value is generally limited to one of only three sources, all of which use as input the trabecular microstructure of an individual measured 25 years ago, and the tissue mass derived from different individuals measured 75 years ago. Our study proposed a new modeling approach to marrow dosimetry---the Paired Image Radiation Transport (PIRT) model---that properly accounts for both the trabecular microstructure and the cortical macrostructure of each skeletal site in a reference male radionuclide patient. The PIRT model, as applied within EGSnrc, requires two sets of input geometry: (1) an infinite voxel array of segmented microimages of the spongiosa acquired via microCT; and (2) a segmented ex-vivo CT image of the bone site macrostructure defining both the spongiosa (marrow, endosteum, and trabeculae) and the cortical bone cortex. Our study also proposed revising reference skeletal dosimetry models for the adult male cancer patient. Skeletal site-specific radionuclide S values were obtained for a 66-year-old male reference patient. The derivation for total skeletal S values were unique in that the necessary skeletal mass and electron dosimetry calculations were formulated from the same source bone site over the entire skeleton. We conclude that paired-image radiation-transport techniques provide an adoptable method by which the intricate, anisotropic trabecular microstructure of the skeletal site; and the physical size and shape of the bone can be handled together, for improved

  15. Expression of mammalian glutathione S-transferase 5-5 in Salmonella typhimurium TA1535 leads to base-pair mutations upon exposure to dihalomethanes.

    PubMed Central

    Thier, R; Taylor, J B; Pemble, S E; Humphreys, W G; Persmark, M; Ketterer, B; Guengerich, F P

    1993-01-01

    Dihalomethanes can produce liver tumors in mice but not in rats, and concern exists about the risk of these compounds to humans. Glutathione (GSH) conjugation of dihalomethanes has been considered to be a critical event in the bioactivation process, and risk assessment is based upon this premise; however, there is little experimental support for this view or information about the basis of genotoxicity. A plasmid vector containing rat GSH S-transferase 5-5 was transfected into the Salmonella typhimurium tester strain TA1535, which then produced active enzyme. The transfected bacteria produced base-pair revertants in the presence of ethylene dihalides or dihalomethanes, in the order CH2Br2 > CH2BrCl > CH2Cl2. However, revertants were not seen when cells were exposed to GSH, CH2Br2, and an amount of purified GSH S-transferase 5-5 (20-fold excess in amount of that expressed within the cells). HCHO, which is an end product of the reaction of GSH with dihalomethanes, also did not produce mutations. S-(1-Acetoxymethyl)GSH was prepared as an analog of the putative S-(1-halomethyl)GSH reactive intermediates. This analog did not produce revertants, consistent with the view that activation of dihalomethanes must occur within the bacteria to cause genetic damage, presenting a model to be considered in studies with mammalian cells. S-(1-Acetoxymethyl)GSH reacted with 2'-deoxyguanosine to yield a major adduct, identified as S-[1-(N2-deoxyguanosinyl)methyl]GSH. Demonstration of the activation of dihalomethanes by this mammalian GSH S-transferase theta class enzyme should be of use in evaluating the risk of these chemicals, particularly in light of reports of the polymorphic expression of a similar activity in humans. Images Fig. 2 PMID:8378332

  16. The presence of an RHD pseudogene containing a 37 base pair duplication and a nonsense mutation in africans with the Rh D-negative blood group phenotype.

    PubMed

    Singleton, B K; Green, C A; Avent, N D; Martin, P G; Smart, E; Daka, A; Narter-Olaga, E G; Hawthorne, L M; Daniels, G

    2000-01-01

    Antigens of the Rh blood group system are encoded by 2 homologous genes, RHD and RHCE, that produce 2 red cell membrane proteins. The D-negative phenotype is considered to result, almost invariably, from homozygosity for a complete deletion of RHD. The basis of all PCR tests for predicting fetal D phenotype from DNA obtained from amniocytes or maternal plasma is detection of the presence of RHD. These tests are used in order to ascertain the risk of hemolytic disease of the newborn. We have identified an RHD pseudogene (RHD psi) in Rh D-negative Africans. RHDpsi contains a 37 base pair (bp) insert in exon 4, which may introduce a stop codon at position 210. The insert is a sequence duplication across the boundary of intron 3 and exon 4. RHDpsi contains another stop codon in exon 6. The frequency of RHDpsi in black South Africans is approximately 0.0714. Of 82 D-negative black Africans, 66% had RHDpsi, 15% had the RHD-CE-D hybrid gene associated with the VS+ V- phenotype, and only 18% completely lacked RHD. RHDpsi is present in about 24% of D-negative African Americans and 17% of D-negative South Africans of mixed race. No RHD transcript could be detected in D-negative individuals with RHDpsi, probably as a result of nonsense-mediated mRNA decay. Existing PCR-based methods for predicting D phenotype from DNA are not suitable for testing Africans or any population containing a substantial proportion of people with African ethnicity. Consequently, we have developed a new test that detects the 37 bp insert in exon 4 of RHDpsi. (Blood. 2000; 95:12-18)

  17. Microhydration of guanine...cytosine base pairs, a theoretical Study on the role of water in stability, structure and tautomeric equilibrium.

    PubMed

    Zelený, Tomás; Hobza, Pavel; Kabelác, Martin

    2009-05-14

    The potential energy surfaces of guanine...cytosine complexes and microhydrated guanine...cytosine (one and two water molecules) were investigated by the molecular dynamics/quenching method (MD/Q), using the empirical potential Parm94 force field, implemented in the Amber program package. The calculations were conducted for all the possible combinations of the four most stable tautomers of guanine and three of cytosine (covering the canonical forms in both cases). The obtained structures were sorted by their structural motifs into three main groups: planar hydrogen-bonded; stacked; and T-shaped structures. The most stable structures found at the empirical potential energy surfaces were fully reoptimised at the second-order Møller-Plesset perturbation theory as well as using the density functional method with an empirical dispersion term (DFT-D). A combination of the canonical form of guanine and cytosine and canonical cytosine with a guanine tautomer where the hydrogen is switched from position N9 to N7 are energetically preferred in microsolvated systems as well as those without the presence of a solvent. The rising number of water molecules leads to smaller differences between the stability of the various combinations of the tautomers of bases in the base pairs. For some of the tautomer combinations (mainly the enol-enol combination), two water molecules are sufficient for the preference of stacked structures over the H-bonded ones. The interaction energies and geometries obtained by the second-order Møller-Plesset perturbation theory method and the much less computationally demanding DFT-D method are comparable, except for stacked complexes, where the interaction energies are overestimated on average by 3 kcal mol(-1) at the MP2 level. PMID:19421545

  18. Binaural unmasking with multiple adjacent masking electrodes in bilateral cochlear implant users

    PubMed Central

    Lu, Thomas; Litovsky, Ruth; Zeng, Fan-Gang

    2011-01-01

    Bilateral cochlear implant (BiCI) users gain an advantage in noisy situations from a second implant, but their bilateral performance falls short of normal hearing listeners. Channel interactions due to overlapping electrical fields between electrodes can impair speech perception, but its role in limiting binaural hearing performance has not been well characterized. To address the issue, binaural masking level differences (BMLD) for a 125 Hz tone in narrowband noise were measured using a pair of pitch-matched electrodes while simultaneously presenting the same masking noise to adjacent electrodes, representing a more realistic stimulation condition compared to prior studies that used only a single electrode pair. For five subjects, BMLDs averaged 8.9 ± 1.0 dB (mean ± s.e.) in single electrode pairs but dropped to 2.1 ± 0.4 dB when presenting noise on adjacent masking electrodes, demonstrating a negative impact of the additional maskers. Removing the masking noise from only the pitch-matched electrode pair not only lowered thresholds but also resulted in smaller BMLDs. The degree of channel interaction estimated from auditory nerve evoked potentials in three subjects was significantly and negatively correlated with BMLD. The data suggest that if the amount of channel interactions can be reduced, BiCI users may experience some performance improvements related to binaural hearing. PMID:21682415

  19. Pyrrolo-dC Metal-Mediated Base Pairs in the Reverse Watson-Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6-Pyridinyl Residues on Fluorescence and Silver-Ion Binding.

    PubMed

    Yang, Haozhe; Mei, Hui; Seela, Frank

    2015-07-01

    Reverse Watson-Crick DNA with parallel-strand orientation (ps DNA) has been constructed. Pyrrolo-dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3-d]pyrimidine base have been incorporated in 12- and 25-mer oligonucleotide duplexes and utilized as silver-ion binding sites. Thermal-stability studies on the parallel DNA strands demonstrated extremely strong silver-ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single (2py) PyrdC-(2py) PyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver-ion base pair that aligns 7-deazapurine bases head-to-tail instead of head-to-head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson-Crick base pairs stabilized by a dinuclear silver-mediated PyrdC pair.

  20. Pyrrolo-dC Metal-Mediated Base Pairs in the Reverse Watson-Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6-Pyridinyl Residues on Fluorescence and Silver-Ion Binding.

    PubMed

    Yang, Haozhe; Mei, Hui; Seela, Frank

    2015-07-01

    Reverse Watson-Crick DNA with parallel-strand orientation (ps DNA) has been constructed. Pyrrolo-dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3-d]pyrimidine base have been incorporated in 12- and 25-mer oligonucleotide duplexes and utilized as silver-ion binding sites. Thermal-stability studies on the parallel DNA strands demonstrated extremely strong silver-ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single (2py) PyrdC-(2py) PyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver-ion base pair that aligns 7-deazapurine bases head-to-tail instead of head-to-head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson-Crick base pairs stabilized by a dinuclear silver-mediated PyrdC pair. PMID:26096946