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Sample records for adjacent base pairs

  1. Adjacent Lone Pair (ALP) Effect: A Computational Approach for Its Origin.

    PubMed

    Zhang, Huaiyu; Wu, Wei; Ahmed, Basil M; Mezei, Gellert; Mo, Yirong

    2016-05-23

    The adjacent lone pair (ALP) effect is an experimental phenomenon in certain nitrogenous heterocyclic systems exhibiting the preference of the products with lone pairs separated over other isomers with lone pairs adjacent. A theoretical elucidation of the ALP effect requires the decomposition of intramolecular energy terms and the isolation of lone pair-lone pair interactions. Here we used the block-localized wavefunction (BLW) method within the ab initio valence bond (VB) theory to derive the strictly localized orbitals which are used to accommodate one-atom centered lone pairs and two-atom centered σ or π bonds. As such, interactions among electron pairs can be directly derived. Two-electron integrals between adjacent lone pairs do not support the view that the lone pair-lone pair repulsion is responsible for the ALP effect. Instead, the disabling of π conjugation greatly diminishes the ALP effect, indicating that the reduction of π conjugation in deprotonated forms with two σ lone pairs adjacent is one of the major causes for the ALP effect. Further electrostatic potential analysis and intramolecular energy decomposition confirm that the other key factor is the favorable electrostatic attraction within the isomers with lone pairs separated. PMID:27139318

  2. A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.

    PubMed

    Chen, Gang; Kennedy, Scott D; Turner, Douglas H

    2009-06-23

    RNA internal loops are often important sites for folding and function. Residues in internal loops can have pKa values shifted close to neutral pH because of the local structural environment. A series of RNA internal loops were studied at different pH by UV absorbance versus temperature melting experiments and imino proton nuclear magnetic resonance (NMR). A stabilizing CA pair forms at pH 7 in the CG/AA and CA/AA nearest neighbors when the CA pair is the first noncanonical pair (loop-terminal pair) in 3 x 3 nucleotide and larger size-symmetric internal loops. These CG/AA and CA/AA nearest neighbors, with CA adjacent to a closing Watson-Crick pair, are further stabilized when the pH is lowered from 7 to 5.5. The results are consistent with a significantly larger fraction (from approximately 20% at pH 7 to approximately 90% at pH 5.5) of adenines being protonated at the N1 position to form stabilizing wobble CA+ pairs adjacent to a sheared GA or AA pair. The noncanonical pair adjacent to the GA pair in CG/AA can either stabilize or destabilize the loop, consistent with the sequence-dependent thermodynamics of GA pairs. No significant pH-dependent stabilization is found for most of the other nearest neighbor combinations involving CA pairs (e.g., CA/AG and AG/CA), which is consistent with the formation of various nonwobble pairs observed in different local sequence contexts in crystal and NMR structures. A revised free-energy model, including stabilization by wobble CA+ pairs, is derived for predicting stabilities of medium-size RNA internal loops. PMID:19485416

  3. Telomere length in hepatocellular carcinoma and paired adjacent non-tumor tissues by quantitative PCR.

    PubMed

    Zhang, Yujing; Shen, Jing; Ming-Whei; Lee, Yu Po-Huang; Santella, Regina M

    2007-12-01

    Telomere shortening limits the proliferative capacity of human cells, restrains the regenerative capacity of organ systems during chronic diseases and aging and also induces chromosomal instability as well as initiation of cancer. Previous studies demonstrated that telomeres are often significantly shorter in tumor tissue, including hepatocellular carcinoma (HCC), compared to the surrounding tissue, but telomere length in HCC tissues was not correlated with several clinical parameters, such as age, sex, HBV or HCV infections and tumor size. In the present study, the telomere length ratio of 36 paired HCC, and their adjacent non-tumor tissues was measured by quantitative PCR (Q-PCR). The mean telomere lengths (SD) for HCC and adjacent non-tumor tissues were 0.26 (0.10) and 0.47 (0.20) respectively (t = 6.22, P < 0.0001). There was a large difference in the distribution of subjects based on telomere length in tumor and adjacent non-tumor tissues. The number of tumors with telomere length shorter than 0.50 was much higher than that of adjacent non-tumor tissues; more than 90% of the tissues with telomere length > or = 0.50 were adjacent non-tumor tissues. The correlations between telomere length and aflatoxin B1- and polycyclic aromatic hydrocarbon-DNA adducts level, p53 mutations and p16 hypermethylation status were also tested, but no significant associations were found. The relationship between telomere length shortening, chemical carcinogen exposure, and genetic and epigenetic changes in hepatocarcinogenesis needs further investigation. PMID:18058461

  4. 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.

  5. 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

  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. 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

  10. 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.

  11. 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.

  12. 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.

  13. Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae ▿

    PubMed Central

    Arnone, James T.; McAlear, Michael A.

    2011-01-01

    The rRNA and ribosome biogenesis (RRB) regulon from Saccharomyces cerevisiae contains some 200 genes, the expression of which is tightly regulated under changing cellular conditions. RRB gene promoters are enriched for the RRPE and PAC consensus motifs, and a significant fraction of RRB genes are found as adjacent gene pairs. A genetic analysis of the MPP10 promoter revealed that both the RRPE and PAC motifs are important for coordinated expression of MPP10 following heat shock, osmotic stress, and glucose replenishment. The association of the RRPE binding factor Stb3 with the MPP10 promoter was found to increase after glucose replenishment and to decrease following heat shock. Similarly, bulk histone H3 clearing and histone H4K12 acetylation levels at the MPP10 promoter were found to increase or decrease following glucose replenishment or heat shock, respectively. Interestingly, substitutions in the PAC and RRPE sequences at the MPP10 promoter were also found to impact the regulated expression of the adjacent RRB gene YJR003, whose promoter lies in the opposite orientation and some 3.8 kb away. Furthermore, the regulated expression of YJR003C could be disrupted by inserting a reporter cassette that increased its distance from MPP10. Given that a high incidence of gene pairing was also found within the ribosomal protein (RP) and RRB regulons across different yeast species, our results indicate that immediately adjacent positioning of genes can be functionally significant for their coregulated expression. PMID:21115740

  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. Base pair analogs in the gas phase.

    PubMed

    Roscioli, Joseph R; Pratt, David W

    2003-11-25

    A rotationally resolved electronic spectrum of the gas-phase dimer 2-aminopyridine.2-pyridone, an analog of the adenine.thymine base pair, has been observed and assigned, leading to precise measurements of its moments of inertia and preliminary determinations of its structure. A Watson-Crick configuration results, with N...H-N and N-H...O hydrogen bond lengths of 2.898 and 2.810 A, respectively. The two bases are found not to be coplanar; a dihedral angle of 6.1 degrees between the base planes is also estimated from the measured moments of inertia. Possible chemical and biological implications of these results are discussed. PMID:14612563

  16. Addendum to "Quantum wireless multihop communication based on arbitrary Bell pairs and teleportation"

    NASA Astrophysics Data System (ADS)

    Wang, Kan; Gong, Yan-Xiao; Yu, Xu-Tao; Lu, Sheng-Li

    2014-10-01

    In our previous work [Phys. Rev. A 89, 022329 (2014), 10.1103/PhysRevA.89.022329], we proposed a teleportation-based quantum communication scheme in a quantum wireless multihop network with arbitrary types of Bell pairs shared between adjacent nodes. Here we revised the scheme by introducing a result-mapping method for halving the classical communication cost, with which the source and intermediate nodes map the measurement outcomes to those corresponding to the target Bell pair type assigned by the destination node. A routing protocol is utilized to piggyback the target Bell pair type notification information which introduces no extra communication cost.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25501592

  18. 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.

  19. 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

  20. Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies.

    PubMed

    Hirao, Ichiro; Kimoto, Michiko; Yamashige, Rie

    2012-12-18

    Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the

  1. 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.

  2. Efficient PCR amplification by an unnatural base pair system.

    PubMed

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

    2008-01-01

    Expansion of the genetic alphabet by an unnatural base pair system enables the site-specific incorporation of extra functional components into nucleic acids and proteins. In this system, PCR amplification of DNA templates containing unnatural base pairs is essential for modern biotechnology. We present a new unnatural base pair system, in which DNA duplexes containing the unnatural base pairs can be efficiently amplified by PCR. The system also provides a method for the site-specific incorporation of functional components into amplified DNA fragments by PCR, using unnatural base substrates linked with functional groups of interest. PMID:18776457

  3. 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.

  4. An ensemble of SVM classifiers based on gene pairs.

    PubMed

    Tong, Muchenxuan; Liu, Kun-Hong; Xu, Chungui; Ju, Wenbin

    2013-07-01

    In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. PMID:23668348

  5. Novel Method for Measuring Structure and Semantic Similarity of XML Documents Based on Extended Adjacency Matrix

    NASA Astrophysics Data System (ADS)

    Zhang, Xue-Liang; Yang, Ting; Fan, Bao-Quan; Wang, Xu; Wei, Jin-Mao

    Similarity measurement of XML documents is crucial to meet various needs of approximate searches and document classifications in XML-oriented applications. Some methods have been proposed for this purpose. Nevertheless, few methods can be elegantly exploited to depict structure and semantic information and hence to effectively measure the similarity of XML documents. In this paper, we present a new method of computing the structure and semantic similarity of XML documents based on extended adjacency matrix(EAM). Different from a general adjacency matrix, in an EAM, the structure information of not only the adjacent layers but also the ancestor-descendant layers can be stored. For measuring the similarity of two XML documents, the proposed method firstly stores the structure and semantic information in two extended adjacency matrices(M1, M2). Then it computes similarity of the two documents through cos(M1, M2) Experimental results on bench-mark data show that the method holds high efficiency and accuracy.

  6. Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine

    PubMed Central

    2016-01-01

    5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5′-CG-3′ sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5′-T8X9G10-3′ sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A5:T8, whereas 5caC did not. At the oxidized base pair G4:X9, 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C3:G10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G4:X9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes. PMID:25632825

  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. A point matching algorithm based on reference point pair

    NASA Astrophysics Data System (ADS)

    Zou, Huanxin; Zhu, Youqing; Zhou, Shilin; Lei, Lin

    2016-03-01

    Outliers and occlusions are important degradation in the real application of point matching. In this paper, a novel point matching algorithm based on the reference point pairs is proposed. In each iteration, it firstly eliminates the dubious matches to obtain the relatively accurate matching points (reference point pairs), and then calculates the shape contexts of the removed points with reference to them. After re-matching the removed points, the reference point pairs are combined to achieve better correspondences. Experiments on synthetic data validate the advantages of our method in comparison with some classical methods.

  9. Calix[4]pyrrole-based ion pair receptors.

    PubMed

    Kim, Sung Kuk; Sessler, Jonathan L

    2014-08-19

    Ion pair receptors, which are able to bind concurrently both a cation and an anion, often display higher selectivity and affinity for specific ion pairs than simple ion receptors capable of recognizing primarily either a cation or an anion. This enhancement in recognition function is attributable to direct or indirect cooperative interactions between cobound ions via electrostatic attractions between oppositely charged ions, as well as to positive allosteric effects. In addition, by virtue of binding the counterions of the targeted ion, ion pair receptors can minimize the solvation of the counterions, which can otherwise have a negative effect on the interactions between the receptors and the targeted ions. As a result of their more favorable interactions, ion pair receptors are attractive for use in applications, such as extraction and sensing, where control of the binding interactions is advantageous. In this Account, we illustrate this potential in the context of ion pair receptors based on the calix[4]pyrrole scaffold. Both simple ditopic ion pair receptors, containing sites for the recognition of a single anion and single cation, and so-called multitopic ion pair receptors will be discussed. The latter systems differ from conventional, so-called ditopic ion pair receptors in that they contain more than one binding site for a given targeted ion (e.g., a cation). This permits a level of selectivity and control over binding function not normally seen for simple ion or ion pair receptors containing one or two binding sites, respectively. Calix[4]pyrroles are macrocyclic compounds consisting of four pyrrole units linked via fully substituted sp(3) hybridized meso carbon atoms. They are effective receptors for Lewis basic anions (e.g., halides) in typical organic media and under certain conditions will recognize ion pairs containing charge diffuse cations, such as a small alkylammonium, imidazolium, or cesium cations. The calix[4]pyrrole framework is further

  10. The 6-thioguanine/5-methyl-2-pyrimidinone base pair.

    PubMed Central

    Rappaport, H P

    1988-01-01

    As part of a program to determine the physical possibility of expanding the number of types of base pairs in DNA, the pairing stabilities of the analog bases 6-thioguanine (GS) and 5-methyl-2-pyrimidinone (TH) in oligodeoxynucleotides were measured. Procedures were developed to synthesize oligodeoxynucleotides with the analog bases. The sequences of the synthesized oligomers were T-C-G-A-C-G-G-X-Y-C-C-G. An enzymatic procedure was developed to measure relative association constants of oligomer pairs with the self complementary reference oligomer, X = A and Y = T, K(T/A) = K. The results were K(C/G) = (5 +/- .5)K, K(TH/GS) = K/(1 +/- .5), K(T/G) = K/(9 +/- 3), K(TH/G) = K/(25 +/- 5), K(C/GS) less than K/30, K(TH/A) less than K/40, K(T/GS) less than K/40, K(C/A) less than K/40. The results with the standard bases are consistent with other methods of measurement. The stability of the base pair GS/TH is approximately the same as the standard base pair A/T. PMID:3412886

  11. Femtosecond molecular dynamics of tautomerization in model base pairs

    NASA Astrophysics Data System (ADS)

    Douhal, A.; Kim, S. K.; Zewail, A. H.

    1995-11-01

    HYDROGEN bonds commonly lend robustness and directionality to molecular recognition processes and supramolecular structures1,2. In particular, the two or three hydrogen bonds in Watson-Crick base pairs bind the double-stranded DNA helix and determine the complementarity of the pairing. Watson and Crick pointed out3, however, that the possible tautomers of base pairs, in which hydrogen atoms become attached to the donor atom of the hydrogen bond, might disturb the genetic code, as the tautomer is capable of pairing with different partners. But the dynamics of hydrogen bonds in general, and of this tautomerization process in particular, are not well understood. Here we report observations of the femtosecond dynamics of tautomerization in model base pairs (7-azaindole dimers) containing two hydrogen bonds. Because of the femtosecond resolution of proton motions, we are able to examine the cooperativity of formation of the tautomer (in which the protons on each base are shifted sequentially to the other base), and to determine the characteristic timescales of the motions in a solvent-free environment. We find that the first step occurs on a timescale of a few hundred femtoseconds, whereas the second step, to form the full tautomer, is much slower, taking place within several picoseconds; the timescales are changed significantly by replacing hydrogen with deuterium. These results establish the molecular basis of the dynamics and the role of quantum tunnelling.

  12. Understanding the kinetic mechanism of RNA single base pair formation

    PubMed Central

    Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

    2016-01-01

    RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. PMID:26699466

  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. Geometric nomenclature and classification of RNA base pairs.

    PubMed Central

    Leontis, N B; Westhof, E

    2001-01-01

    Non-Watson-Crick base pairs mediate specific interactions responsible for RNA-RNA self-assembly and RNA-protein recognition. An unambiguous and descriptive nomenclature with well-defined and nonoverlapping parameters is needed to communicate concisely structural information about RNA base pairs. The definitions should reflect underlying molecular structures and interactions and, thus, facilitate automated annotation, classification, and comparison of new RNA structures. We propose a classification based on the observation that the planar edge-to-edge, hydrogen-bonding interactions between RNA bases involve one of three distinct edges: the Watson-Crick edge, the Hoogsteen edge, and the Sugar edge (which includes the 2'-OH and which has also been referred to as the Shallow-groove edge). Bases can interact in either of two orientations with respect to the glycosidic bonds, cis or trans relative to the hydrogen bonds. This gives rise to 12 basic geometric types with at least two H bonds connecting the bases. For each geometric type, the relative orientations of the strands can be easily deduced. High-resolution examples of 11 of the 12 geometries are presently available. Bifurcated pairs, in which a single exocyclic carbonyl or amino group of one base directly contacts the edge of a second base, and water-inserted pairs, in which single functional groups on each base interact directly, are intermediate between two of the standard geometries. The nomenclature facilitates the recognition of isosteric relationships among base pairs within each geometry, and thus facilitates the recognition of recurrent three-dimensional motifs from comparison of homologous sequences. Graphical conventions are proposed for displaying non-Watson-Crick interactions on a secondary structure diagram. The utility of the classification in homology modeling of RNA tertiary motifs is illustrated. PMID:11345429

  15. 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

  16. The thermodynamics and kinetics of a nucleotide base pair.

    PubMed

    Wang, Yujie; Gong, Sha; Wang, Zhen; Zhang, Wenbing

    2016-03-21

    The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian. PMID:27004898

  17. The thermodynamics and kinetics of a nucleotide base pair

    NASA Astrophysics Data System (ADS)

    Wang, Yujie; Gong, Sha; Wang, Zhen; Zhang, Wenbing

    2016-03-01

    The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.

  18. Ultrafast dynamics in DNA base pairs following ultraviolet excitation.

    NASA Astrophysics Data System (ADS)

    Orr-Ewing, Andrew

    2015-03-01

    Photo-protective mechanisms in DNA are essential to maintain the integrity of the genetic code by preventing damage from absorption of solar ultraviolet (UV) radiation. We have used time-resolved infra-red (TRIR) spectroscopy to observe the dynamics of Watson-Crick nucleobase pairs following absorption of femtosecond UV laser pulses. The base pairs are prepared as nucleosides in solution, and photo-induced dynamics are probed in the carbonyl and N-H bond stretching regions using broadband IR pulses with picosecond time resolution. Results will be presented for the guanine-cytosine (G-C) base pair, contrasting the rapid recovery of ground-state products (the photo-protection pathway) with formation of other photoproducts which might represent photo-damage mechanisms. This work is a collaboration with the group of Prof F. Temps (Christian-Albrechts-Universitat zu Kiel). This research is supported by ERC Advanced Grant 290966 CAPRI.

  19. Systematic Detection of Epistatic Interactions Based on Allele Pair Frequencies

    PubMed Central

    Ackermann, Marit; Beyer, Andreas

    2012-01-01

    Epistatic genetic interactions are key for understanding the genetic contribution to complex traits. Epistasis is always defined with respect to some trait such as growth rate or fitness. Whereas most existing epistasis screens explicitly test for a trait, it is also possible to implicitly test for fitness traits by searching for the over- or under-representation of allele pairs in a given population. Such analysis of imbalanced allele pair frequencies of distant loci has not been exploited yet on a genome-wide scale, mostly due to statistical difficulties such as the multiple testing problem. We propose a new approach called Imbalanced Allele Pair frequencies (ImAP) for inferring epistatic interactions that is exclusively based on DNA sequence information. Our approach is based on genome-wide SNP data sampled from a population with known family structure. We make use of genotype information of parent-child trios and inspect 3×3 contingency tables for detecting pairs of alleles from different genomic positions that are over- or under-represented in the population. We also developed a simulation setup which mimics the pedigree structure by simultaneously assuming independence of the markers. When applied to mouse SNP data, our method detected 168 imbalanced allele pairs, which is substantially more than in simulations assuming no interactions. We could validate a significant number of the interactions with external data, and we found that interacting loci are enriched for genes involved in developmental processes. PMID:22346757

  20. Social Networks-Based Adaptive Pairing Strategy for Cooperative Learning

    ERIC Educational Resources Information Center

    Chuang, Po-Jen; Chiang, Ming-Chao; Yang, Chu-Sing; Tsai, Chun-Wei

    2012-01-01

    In this paper, we propose a grouping strategy to enhance the learning and testing results of students, called Pairing Strategy (PS). The proposed method stems from the need of interactivity and the desire of cooperation in cooperative learning. Based on the social networks of students, PS provides members of the groups to learn from or mimic…

  1. Deformability-based microfluidic cell pairing and fusion.

    PubMed

    Dura, Burak; Liu, Yaoping; Voldman, Joel

    2014-08-01

    We present a microfluidic cell pairing device capable of sequential trapping and pairing of hundreds of cells using passive hydrodynamics and flow-induced deformation. We describe the design and operation principles of our device and show its applicability for cell fusion. Using our device, we achieved both homotypic and heterotypic cell pairing, demonstrating efficiencies up to 80%. The platform is compatible with fusion protocols based on biological, chemical and physical stimuli with fusion yields up to 95%. Our device further permits its disconnection from the fluidic hardware enabling its transportation for imaging and culture while maintaining cell registration on chip. Our design principles and cell trapping technique can readily be applied for different cell types and can be extended to trap and fuse multiple (>2) cell partners as demonstrated by our preliminary experiments. PMID:24898933

  2. Configurations of base-pair complexes in solutions. [nucleotide chemistry

    NASA Technical Reports Server (NTRS)

    Egan, J. T.; Nir, S.; Rein, R.; Macelroy, R.

    1978-01-01

    A theoretical search for the most stable conformations (i.e., stacked or hydrogen bonded) of the base pairs A-U and G-C in water, CCl4, and CHCl3 solutions is presented. The calculations of free energies indicate a significant role of the solvent in determining the conformations of the base-pair complexes. The application of the continuum method yields preferred conformations in good agreement with experiment. Results of the calculations with this method emphasize the importance of both the electrostatic interactions between the two bases in a complex, and the dipolar interaction of the complex with the entire medium. In calculations with the solvation shell method, the last term, i.e., dipolar interaction of the complex with the entire medium, was added. With this modification the prediction of the solvation shell model agrees both with the continuum model and with experiment, i.e., in water the stacked conformation of the bases is preferred.

  3. Recognition of base pair inversions in duplex by chimeric (alpha,beta) triplex-forming oligonucleotides.

    PubMed

    Timofeev, Edward N; Goryaeva, Baira V; Florentiev, Vladimir L

    2006-10-01

    DNA recognition by triplex-forming oligonucleotides (TFOs) is usually limited by homopurine-homopyrimidine sequence in duplexes. Modifications of the third strand may overcome this limitation. Chimeric alpha-beta TFOs are expected to form triplex DNA upon binding to non-regular sequence duplexes. In the present study we describe binding properties of chimeric alpha-beta oligodeoxynucleotides in the respect to short DNA duplexes with one, three, and five base pair inversions. Non-natural chimeric TFO's contained alpha-thymidine residues inside (GT) or (GA) core sequences. Modified residues were addressed to AT/TA inversions in duplexes. It was found in the non-denaturing gel-electrophoresis experiments that single or five adjacent base pair inversions in duplexes may be recognized by chimeric alpha-beta TFO's at 10 degrees C and pH 7.8. Three dispersed base pair inversions in the double stranded DNA prevented triplex formation by either (GT) or (GA) chimeras. Estimation of thermal stability of chimeric alpha-beta triplexes showed decrease in T(m) values as compared with unmodified complexes. PMID:16928141

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    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.

  5. 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.

  6. 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

  7. Cell pairing using microwell array electrodes based on dielectrophoresis.

    PubMed

    Yoshimura, Yuki; Tomita, Masahiro; Mizutani, Fumio; Yasukawa, Tomoyuki

    2014-07-15

    We report a simple device with an array of 10,000 (100 × 100) microwells for producing vertical pairs of cells in individual microwells with a rapid manipulation based on positive dielectrophoresis (p-DEP). The areas encircled with micropoles which fabricated from an electrical insulating photosensitive polymer were used as microwells. The width (14 μm) and depth (25 μm) of the individual microwells restricted the size to two vertically aligned cells. The DEP device for the manipulation of cells consisted of a microfluidic channel with an upper indium tin oxide (ITO) electrode and a lower microwell array electrode fabricated on an ITO substrate. Mouse myeloma cells stained in green were trapped within 1 s in the microwells by p-DEP by applying an alternating current voltage between the upper ITO and the lower microwell array electrode. The cells were retained inside the wells even after switching off the voltage and washing with a fluidic flow. Other myeloma cells stained in blue were then trapped in the microwells occupied by the cells stained in green to form the vertical cell pairing in the microwells. Cells stained in different colors were paired within only 1 min and a pairing efficiency of over 50% was achieved. PMID:24947270

  8. Synthesis, base pairing and structure studies of geranylated RNA.

    PubMed

    Wang, Rui; Vangaveti, Sweta; Ranganathan, Srivathsan V; Basanta-Sanchez, Maria; Haruehanroengra, Phensinee; Chen, Alan; Sheng, Jia

    2016-07-27

    Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNA(Glu) UUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon-anticodon interaction during ribosome binding. PMID:27307604

  9. 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.

  10. 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

  11. Charge Transport in DNA with Five Base Pairs

    NASA Astrophysics Data System (ADS)

    Lee, Sunhee; Hedin, Eric; Joe, Yong

    2008-10-01

    Recently, much interest has arisen in the process of charge transport through DNA due to its fundamental roles in biological processes and in possible novel molecular electronics. We investigate quantum mechanical electron transmission along the long axis of the DNA molecule using a one-dimensional tight-binding model. In this system, we consider a single central conduction channel in which individual sites represent a base-pair formed by either AT (TA) or GC (CG) pairs coupled via hydrogen bonds. The sites are linked by a hopping amplitude, or quantum overlap integral. The sugar-phosphate backbone and the hopping amplitude between each site of the base and the backbone are incorporated into an energy-dependent on-site potential in the main DNA site. For the sake of simplicity, a simple DNA molecule segment with five base pairs is studied, and the transmission for different values of on-site energy is calculated to determine the influence of mismatch (impurity) effects in the DNA sequence. Finally, we present results for the temperature dependence of the transmission, and the current-voltage characteristics in order to examine the extent and efficiency of charge migration. *One of the authors (E.R.H) is partially supported by a grant from the Center for Energy Research, Education, and Service (CERES) at Ball State University.

  12. Graphene/Lead (Pb)-based Cooper -pair splitter

    NASA Astrophysics Data System (ADS)

    Borzenets, Ivan; Shimazaki, Yuya; Jones, Gareth; Russo, Saverio; Yamamoto, Michihisa; Tarucha, Seigo

    2015-03-01

    We have fabricated a Cooper-pair splitter device based on a superconductor- two normal leads, ``Y'' shaped junction with graphene as the base material. (Compared to nanowire-based devices, the two dimensional nature of graphene allows for the normal leads to be placed arbitrarily close together and in a non-parallel arrangement.) The superconducting lead is created by contacting graphene with lead (Pb), thus inducing a supercurrent via the proximity effect. The normal metal leads are patterned into quantum dots by etching nano-constrictions with self-aligned side gates. Quantum dots strongly suppress two electron processes, allowing only one electron to pass at a time. Thus, the Cooper-pair splitting efficiency is enhanced as the split electrons must necessarily tunnel through different quantum dots. Using a DC measurement we have demonstrated enhanced currents though both normal leads when both quantum dots are in resonance and the input lead is in the superconducting regime: demonstrating Cooper-pair splitting. (This is contrary to the classical regime of currents though a three resistor junction.) Shot noise measurements would demonstrate that the split electrons tunnel at the same time. Demonstrating that the split electrons have opposite spin would show that such a device could be used as a source of quantum entangled electrons.

  13. 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

  14. Coherent Pair Production in Deformed Crystals with a Complex Base

    NASA Astrophysics Data System (ADS)

    Mkrtchyan, A. R.; Saharian, A. A.; Parazian, V. V.

    We investigate the coherent electron-positron pair creation by high-energy photons in a periodically deformed single crystal with a complex base. The formula for the corresponding differential cross-section is derived for an arbitrary deformation field. The conditions are specified under which the influence of the deformation is considerable. The case is considered in detail when the photon enters into the crystal at small angles with respect to a crystallographic axis. The results of the numerical calculations are presented for SiO2 single crystal and Moliere parametrization of the screened atomic potentials in the case of the deformation field generated by the acoustic wave of S type. In dependence of the parameters, the presence of deformation can either enhance or reduce the pair creation cross-section. This can be used to control the parameters of the positron sources for storage rings and colliders.

  15. 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.

  16. 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.

  17. Constructing optimal backbone segments for joining fixed DNA base pairs.

    PubMed Central

    Mazur, J; Jernigan, R L; Sarai, A

    1996-01-01

    A method is presented to link a sequence of space-fixed base pairs by the sugar-phosphate segments of single nucleotides and to evaluate the effects in the backbone caused by this positioning of the bases. The entire computational unit comprises several nucleotides that are energy-minimized, subject to constraints imposed by the sugar-phosphate backbone segments being anchored to space-fixed base pairs. The minimization schemes are based on two stages, a conjugate gradient method followed by a Newton-Raphson algorithm. Because our purpose is to examine the response, or relaxation, of an artificially stressed backbone, it is essential to be able to obtain, as closely as possible, a lowest minimum energy conformation of the backbone segment in conformational space. For this purpose, an algorithm is developed that leads to the generation of an assembly of many local energy minima. From these sets of local minima, one conformation corresponding to the one with the lowest minimum is then selected and designated to represent the backbone segment at its minimum. The effective electrostatic potential of mean force is expressed in terms of adjustable parameters that incorporate solvent screening action in the Coulombic interactions between charged backbone atoms; these parameters are adjusted to obtain the best fit of the nearest-neighbor phosphorous atoms in an x-ray structure. PMID:8874023

  18. Conserved arginines on the rim of Hfq catalyze base pair formation and exchange

    PubMed Central

    Panja, Subrata; Schu, Daniel J.; Woodson, Sarah A.

    2013-01-01

    The Sm-like protein Hfq is required for gene regulation by small RNAs (sRNAs) in bacteria and facilitates base pairing between sRNAs and their mRNA targets. The proximal and distal faces of the Hfq hexamer specifically bind sRNA and mRNA targets, but they do not explain how Hfq accelerates the formation and exchange of RNA base pairs. Here, we show that conserved arginines on the outer rim of the hexamer that are known to interact with sRNA bodies are required for Hfq’s chaperone activity. Mutations in the arginine patch lower the ability of Hfq to act in sRNA regulation of rpoS translation and eliminate annealing of natural sRNAs or unstructured oligonucleotides, without preventing binding to either the proximal or distal face. Stopped-flow FRET and fluorescence anisotropy show that complementary RNAs transiently form a ternary complex with Hfq, but the RNAs are not released as a double helix in the absence of rim arginines. RNAs bound to either face of Hfq quench the fluorescence of a tryptophan adjacent to the arginine patch, demonstrating that the rim can simultaneously engage two RNA strands. We propose that the arginine patch overcomes entropic and electrostatic barriers to helix nucleation and constitutes the active site for Hfq’s chaperone function. PMID:23771143

  19. 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.

  20. 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…

  1. Nonclassically paired photons from sources based on cold atoms

    NASA Astrophysics Data System (ADS)

    Głódź, Małgorzata; Janowicz, Maciej; Kowalski, Krzysztof; Szonert, Jerzy

    2015-01-01

    In this short review some essentials concerning creation and testing of nonclassically correlated photons (biphotons) are given. In the introduction we remind the role which the experimentally produced entangled states have been playing for the foundations of the quantum physics, by witnessing against the model of local hidden variables. The well established sources of biphotons are based on spontaneous parametric down conversion in nonlinear crystals. A popular source with two BBO crystals is described, which generates pairs of photons nearly maximally entangled in polarization. Crystalbased sources rely on intrinsically broadband transitions, therefore thus produced biphotons are also broadband. Additional efforts (like applying optical cavities) are needed to reach narrowband biphotons which would comply with the requirements of some implementations in the quantum communication science. The topical issue of our article is a review of another, more recent approaches based on narrowband transitions between levels in cold atoms. Such method provides naturally narrowband biphotons. First, the principles are given of an atomic source of nonclassically paired photons, which is operated in a pulsed write-read mode. Such source is based on two separated in time Raman transitions triggered successively in two Λ-schemes. Next, cw-mode sources based (mainly) on spontaneous four wave mixing process (SFWM) are presented in a generic four-level scheme. Some underlying physics is sketched and profiles of biphoton correlation functions in the time domain are explained. Among other presented SFWM sources, one proves in testing high degree entanglement of generated biphotons, both in time-frequency and polarization (hyperentanglement).

  2. 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%. PMID:15936021

  3. Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies.

    PubMed

    Roy, Ashim; Panigrahi, Swati; Bhattacharyya, Malyasri; Bhattacharyya, Dhananjay

    2008-03-27

    The importance of non-Watson-Crick base pairs in the three-dimensional structure of RNA is now well established. The structure and stability of these noncanonical base pairs are, however, poorly understood. We have attempted to understand structural features of 33 frequently occurring base pairs using density functional theory. These are of three types, namely (i) those stabilized by two or more polar hydrogen bonds between the bases, (ii) those having one polar and another C-H...O/N type interactions, and (iii) those having one H-bond between the bases and another involving one of the sugars linked to the bases. We found that the base pairs having two polar H-bonds are very stable as compared to those having one C-H...O/N interaction. Our quantitatively analysis of structures of these optimized base pairs indicates that they possess a different amount of nonplanarity with large propeller or buckle values as also observed in the crystal structures. We further found that geometry optimization does not modify the hydrogen-bonding pattern, as values of shear and open angle of the base pairs remain conserved. The structures of initial crystal geometry and final optimized geometry of some base pairs having only one polar H-bond and a C-H...O/N interaction, however, are significantly different, indicating the weak nature of the nonpolar interaction. The base pair flexibility, as measured from normal-mode analysis, in terms of the intrinsic standard deviations of the base pair structural parameters are in conformity with those calculated from RNA crystal structures. We also noticed that deformation of a base pair along the stretch direction is impossible for all of the base pairs, and movements of the base pairs along shear and open are also quite restricted. The base pair opening mode through alteration of propeller or buckle is considerably less restricted for most of the base pairs. PMID:18318519

  4. 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

  5. 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

  6. Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA.

    PubMed

    Vengut-Climent, Empar; Gómez-Pinto, Irene; Lucas, Ricardo; Peñalver, Pablo; Aviñó, Anna; Fonseca Guerra, Célia; Bickelhaupt, F Matthias; Eritja, Ramón; González, Carlos; Morales, Juan C

    2016-07-18

    Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside-RNA recognition, glucose-nucleobase pairs have been examined. Deoxyoligonucleotides with a 6-deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6-Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6-deoxyglucose-guanine pair closely resembles a purine-pyrimidine geometry. Quantum chemical calculations indicate that glucose-purine pairs are as stable as a natural T-A pair. PMID:27328804

  7. Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing

    PubMed Central

    van Nues, Robert Willem; Granneman, Sander; Kudla, Grzegorz; Sloan, Katherine Elizabeth; Chicken, Matthew; Tollervey, David; Watkins, Nicholas James

    2011-01-01

    2′-O-methylation of eukaryotic ribosomal RNA (r)RNA, essential for ribosome function, is catalysed by box C/D small nucleolar (sno)RNPs. The RNA components of these complexes (snoRNAs) contain one or two guide sequences, which, through base-pairing, select the rRNA modification site. Adjacent to the guide sequences are protein-binding sites (the C/D or C′/D′ motifs). Analysis of >2000 yeast box C/D snoRNAs identified additional conserved sequences in many snoRNAs that are complementary to regions adjacent to the rRNA methylation site. This ‘extra base-pairing' was also found in many human box C/D snoRNAs and can stimulate methylation by up to five-fold. Sequence analysis, combined with RNA–protein crosslinking in Saccharomyces cerevisiae, identified highly divergent box C′/D′ motifs that are bound by snoRNP proteins. In vivo rRNA methylation assays showed these to be active. Our data suggest roles for non-catalytic subunits (Nop56 and Nop58) in rRNA binding and support an asymmetric model for box C/D snoRNP organization. The study provides novel insights into the extent of the snoRNA–rRNA interactions required for efficient methylation and the structural organization of the snoRNPs. PMID:21556049

  8. Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism

    PubMed Central

    Yusupov, Marat; Yusupova, Gulnara

    2014-01-01

    The natural bases of nucleic acids have a strong preference for one tautomer form, guaranteeing fidelity in their hydrogen bonding potential. However, base pairs observed in recent crystal structures of polymerases and ribosomes are best explained by an alternative base tautomer, leading to the formation of base pairs with Watson-Crick-like geometries. These observations set limits to geometric selection in molecular recognition of complementary Watson-Crick pairs for fidelity in replication and translation processes. PMID:24765524

  9. Fixed-base comb with window-non-adjacent form (NAF) method for scalar multiplication.

    PubMed

    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

  10. 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

  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. 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

  13. 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.

  14. 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

  15. Effect of nucleobase sequence on the proton-transfer reaction and stability of the guanine-cytosine base pair radical anion.

    PubMed

    Chen, Hsing-Yin; Yeh, Shu-Wen; Hsu, Sodio C N; Kao, Chai-Lin; Dong, Teng-Yuan

    2011-02-21

    The formation of base pair radical anions is closely related to many fascinating research fields in biology and chemistry such as radiation damage to DNA and electron transport in DNA. However, the relevant knowledge so far mainly comes from studies on isolated base pair radical anions, and their behavior in the DNA environment is less understood. In this study, we focus on how the nucleobase sequence affects the properties of the guanine-cytosine (GC) base pair radical anion. The energetic barrier and reaction energy for the proton transfer along the N(1)(G)-H···N(3)(C) hydrogen bond and the stability of GC˙(-) (i.e., electron affinity of GC) embedded in different sequences of base-pair trimer were evaluated using density functional theory. The computational results demonstrated that the presence of neighboring base pairs has an important influence on the behavior of GC˙(-) in the gas phase. The excess electron was found to be localized on the embedded GC and the charge leakage to neighboring base pairs was very minor in all of the investigated sequences. Accordingly, the sequence behavior of the proton-transfer reaction and the stability of GC˙(-) is chiefly governed by electrostatic interactions with adjacent base pairs. However, the effect of base stacking, due to its electrostatic nature, is severely screened upon hydration, and thus, the sequence dependence of the properties of GC˙(-) in aqueous environment becomes relatively weak and less than that observed in the gas phase. The effect of geometry relaxation associated with neighboring base pairs as well as the possibility of proton transfer along the N(2)(G)-H···O(2)(C) channel have also been investigated. The implications of the present findings to the electron transport and radiation damage of DNA are discussed. PMID:21152551

  16. 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.

  17. 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

  18. Reversed-phase ion-pair liquid chromatography method for purification of duplex DNA with single base pair resolution

    PubMed Central

    Wysoczynski, Christina L.; Roemer, Sarah C.; Dostal, Vishantie; Barkley, Robert M.; Churchill, Mair E. A.; Malarkey, Christopher S.

    2013-01-01

    Obtaining quantities of highly pure duplex DNA is a bottleneck in the biophysical analysis of protein–DNA complexes. In traditional DNA purification methods, the individual cognate DNA strands are purified separately before annealing to form DNA duplexes. This approach works well for palindromic sequences, in which top and bottom strands are identical and duplex formation is typically complete. However, in cases where the DNA is non-palindromic, excess of single-stranded DNA must be removed through additional purification steps to prevent it from interfering in further experiments. Here we describe and apply a novel reversed-phase ion-pair liquid chromatography purification method for double-stranded DNA ranging in lengths from 17 to 51 bp. Both palindromic and non-palindromic DNA can be readily purified. This method has the unique ability to separate blunt double-stranded DNA from pre-attenuated (n-1, n-2, etc) synthesis products, and from DNA duplexes with single base pair overhangs. Additionally, palindromic DNA sequences with only minor differences in the central spacer sequence of the DNA can be separated, and the purified DNA is suitable for co-crystallization of protein–DNA complexes. Thus, double-stranded ion-pair liquid chromatography is a useful approach for duplex DNA purification for many applications. PMID:24013567

  19. Choline Ions Stabilize A-T Base Pairs by Fitting into Minor Groove

    NASA Astrophysics Data System (ADS)

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

    In a Watson-Crick base paired DNA duplex, G-C base pairs are more stable than A-T base pairs. However, in solvent containing choline ions, the stabilities of these base pairs are reversed. To elucidate the mechanism through which choline ions exert this effect from a microscopic viewpoint, we performed molecular dynamics simulations. We found that choline ions interact with a DNA duplex through multiple hydrogen bonds. The affinity of choline ion for the minor groove of A-T base pairs was higher than that for the major groove. The binding of choline ions to the minor groove of A-T base pairs supports groove formation without disturbing the formation of hydrogen bonds between the base pairs. In contrast, choline ions inhibit the formation of hydrogen bonds between G-C base pairs by binding to atoms of these bases that are involved in Watson-Crick hydrogen bonding. These findings will help us understand the stabilities of canonical DNA structures under the crowded conditions inside cells.

  20. Development of artificial nucleic acid that recognizes a CG base pair in triplex DNA formation.

    PubMed

    Hari, Yoshiyuki

    2013-01-01

    An oligonucleotide that can form a triplex with double-stranded DNA is called a triplex-forming oligonucleotide (TFO). TFOs have gained considerable attention because of their potential as gene targeting tools. However, triplex DNA formation involves inherent problems for practical use. The most important problem is that natural nucleotides in TFO do not have sufficient affinity and base pair-selectivity to pyrimidine-purine base pair, like a CG or TA base pair, within dsDNA. This suggests that dsDNA region including a CG or TA base pair cannot be targeted. Therefore, artificial nucleotides, especially with non-natural nucleobases, capable of direct recognition of a CG or TA base pair via hydrogen bond formation have been developed; however, nucleotides with better selectivity and stronger affinity are necessary for implementing this dsDNA-targeting technology using TFOs. Under such a background, we considered that facile and efficient synthesis of various nucleobase derivatives in TFOs would be useful for finding an ideal nucleobase for recognition of a CG or TA base pair because detailed and rational exploration of nucleobase structures is facilitated. Recently, to develop a nucleobase recognizing a CG base pair, we have used post-elongation modification, i.e., modification after oligonucleotide synthesis, for the facile synthesis of nucleobase derivatives. This review mainly summarizes our recent findings on the development of artificial nucleobases and nucleotides for recognition of a CG base pair in triplexes formed between dsDNA and TFOs. PMID:24189561

  1. Conducting Task-Based Interviews with Pairs of Children: Consensus, Conflict, Knowledge Construction and Turn Taking

    ERIC Educational Resources Information Center

    Houssart, Jenny; Evens, Hilary

    2011-01-01

    This article explores theoretical and methodological issues associated with task-based interviews conducted with pairs of children. We explore different approaches to interviews from sociological, psychological and subject-based perspectives. Our interviews, concerning mathematical questions and carried out with pairs of 10 and 11-year-olds, are…

  2. 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…

  3. Contrasts Between Precipitation over Mediterranean Sea and Adjacent Continental Areas Based on Decadal Scale Satellite Estimates

    NASA Technical Reports Server (NTRS)

    Smith, Eric A.

    2007-01-01

    Most knowledge concerning the last century's climatology and climate dynamics of precipitation over the Mediterranean Sea basin is based on observations taken from rain gauges surrounding the sea itself. In turn, most of the observations come from Southern Europe, with many fewer measurements taken from widely scattered sites situated over North Africa, the Middle East, and the Balkans. This aspect of research on the Mediterranean Sea basin is apparent in a recent compilation of studies presented in book form concerning climate variability of the Mediterranean region [Lionello, P., P. Malanotte-Rizzoli, and R. Boscolo (eds.), 2006: Mediterranean Climate Variability. Elsevier, Amsterdam, 9 chapters.] In light of this missing link to over-water observations, this study (in conjunction with four companion studies by Z. Haddad, A. Mugnai, T. Nakazawa, and G. Stephens) will contrast the nature of precipitation variability directly over the Mediterranean Sea to precipitation variability over the surrounding land areas based on three decades of satellite-based precipitation estimates which have stood up well to validation scrutiny. The satellite observations are drawn from the Global Precipitation Climatology Project (GPCP) dataset extending back to 1979 and the TRMM Merged Algorithm 3b42 dataset extending back to 1998. Both datasets are mostly produced from microwave measurements, excepting the period from 1979 to mid-1987 when only infrared satellite measurements were available for the GPCP estimates. The purpose of this study is to emphasize how the salient properties of precipitation variability over land and sea across a hierarchy of space and time scales, and the salient differences in these properties, might be used in guiding short-term climate models to better predictions of future climate states under different regional temperature-change scenarios.

  4. 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

  5. Non-classical logic inverter coupling a ZnO nanowire-based Schottky barrier transistor and adjacent Schottky diode.

    PubMed

    Hosseini Shokouh, Seyed Hossein; Raza, Syed Raza Ali; Lee, Hee Sung; Im, Seongil

    2014-08-21

    On a single ZnO nanowire (NW), we fabricated an inverter-type device comprising a Schottky diode (SD) and field-effect transistor (FET), aiming at 1-dimensional (1D) electronic circuits with low power consumption. The SD and adjacent FET worked respectively as the load and driver, so that voltage signals could be easily extracted as the output. In addition, NW FET with a transparent conducting oxide as top gate turned out to be very photosensitive, although ZnO NW SD was blind to visible light. Based on this, we could achieve an array of photo-inverter cells on one NW. Our non-classical inverter is regarded as quite practical for both logic and photo-sensing due to its performance as well as simple device configuration. PMID:24985947

  6. 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.

  7. 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.

  8. Thermodynamics of the formation of Ag(I)-mediated azole base pairs in DNA duplexes.

    PubMed

    Schweizer, Kristina; Léon, J Christian; Ravoo, Bart Jan; Müller, Jens

    2016-07-01

    Isothermal titration calorimetry was applied to determine the thermodynamic parameters for the specific binding of Ag(I) ions to a series of DNA duplexes comprising Im:Im or Tr:Tr mispairs to form metal-mediated Im-Ag(I)-Im or Tr-Ag(I)-Tr base pairs (Im=imidazole nucleoside; Tr=1.2,4-triazole nucleoside). A total of seven different duplexes are discussed, incorporating one to three artificial base pairs in neighboring or non-neighboring positions. The association constant related to the formation of Tr-Ag(I)-Tr base pairs is estimated to be <10(3)M(-1). In contrast, Im-Ag(I)-Im base pairs are much more stable. The intrinsic association constant for their formation is in the order of 10(6)M(-1) and is therefore larger than that for the formation of T-Hg(II)-T and C-Ag(I)-C base pairs consisting of natural nucleobases. Two neighboring Im-Ag(I)-Im base pairs form cooperatively, whereas two remotely located Im-Ag(I)-Im base pairs form non-cooperatively. In general, the specific binding of Ag(I) to Im:Im-containing duplexes is enthalpically driven, with a significant additional entropic contribution in most cases. PMID:27032292

  9. An essential non-Watson-Crick base pair motif in 3'UTR to mediate selenoprotein translation.

    PubMed Central

    Walczak, R; Carbon, P; Krol, A

    1998-01-01

    The SECIS element is an RNA hairpin in the 3'UTR of selenoprotein mRNAs required for decoding UGA selenocysteine codons. Our experimentally derived 2D structure model for the SECIS RNA revealed the conservation of four consecutive non-Watson-Crick base pairs, with a central G.A/A.G tandem. The present study was dedicated to gaining insight into the role of this quartet of base pairs. The effects of mutations introduced into the SECIS quartet of the glutathione peroxidase (GPx) cDNA, an enzyme with selenocysteine in its active center, were reported in vivo by the GPx activity. The detrimental consequence of an all-Watson-Crick mutant quartet disclosed the paramount importance of the non-Watson-Crick base pairs for GPx activity. Next, structure probing established that base pair changes in the central G.A/A.G tandem, predicted by the model to be structurally unfavorable, effectively led to local opening of the helix at the quartet. A concomitant abolition of GPx activity was observed, arising from translational impairment of full-length GPx. In contrast, an isosteric base pair replacement in the tandem did not affect base pairing in the quartet, leading to an almost wt GPx activity. Collectively, the data provided conclusive evidence for the functional relevance of these non-Watson-Crick base pairs in vivo, thus identifying a noncanonical RNA motif crucial to SECIS function in mediating selenoprotein translation. Within the quartet, the prominent requirement for the central G.A/A.G tandem is highlighted, our previous structural model and the mutagenesis data presented here strongly arguing in favor of a sheared arrangement for the G.A base pairs. The SECIS RNA is therefore another member to be added to the growing list of RNAs containing building blocks of non-Watson-Crick base pairs, required for structure and/or function. PMID:9436910

  10. Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins

    PubMed Central

    Renaud, Nicolas; Berlin, Yuri A.; Ratner, Mark A.

    2013-01-01

    Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here. Instead of the phenomenological two-step hopping mechanism via the guanine base, the charge propagation occurs through a delocalization of the hole density along the base pair stack. Furthermore, the variations of the charge transfer with the position of the guanine base are explained by the impact of the base pair substitutions on the delocalized conduction channels. PMID:23980166

  11. 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. PMID:26856595

  12. SURVEY AND SUMMARY: The non-Watson–Crick base pairs and their associated isostericity matrices

    PubMed Central

    Leontis, Neocles B.; Stombaugh, Jesse; Westhof, Eric

    2002-01-01

    RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson–Crick base pairing, forming motifs that mediate long-range RNA–RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson–Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 × 4 ‘isostericity matrices’ summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 Å resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs. PMID:12177293

  13. Isomers of the DNA bases and their possible role in base pair mismatch

    NASA Astrophysics Data System (ADS)

    Michaelian, Karo; Romero, Aldo

    2004-03-01

    We have found stable isomers of the two DNA purines, adenine and guanine, in global searches using a force field potential and ab initio local relaxations. The stability characteristics were investigated by searching for the lowest energy connecting saddles, and by using Car-Parrinello molecular dynamics. Expected equilibrium concentrations and possible non-equilibrium production mechanisms are discussed. It is suggested that these isomers may play a role in base-pair miss-match leading to point mutation of the gnome, and in a number of other important biological processes based on the purine structures.

  14. 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

  15. 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

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

    PubMed

    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

  18. Structural Implications of Homopyrimidine Base Pairs in the Parallel-Stranded d(YGA) Motif.

    PubMed

    Tripathi, Shailesh; Paukstelis, Paul J

    2016-06-16

    DNA can adopt many other structures beyond the canonical B-form double helix. These alternative DNA structures have become increasingly significant as new biological roles are found for them. Additionally, there has been a growing interest in using non-canonical base pairs to provide structural diversity for designing DNA architectures for nanotechnology applications. We recently described the crystal structure of d(ACTCGGATGAT), which forms a tetraplex through parallel-stranded homo-base pairs and nucleobase intercalation. The homoduplex region contains a d(YGA⋅YGA) motif observed in crystal and solution structures. Here, we examine the structural implications of the homopyrimidine base pair within this motif. We determined crystal structures of two variants that differ from the original structure in the homopyrimidine base pairs and number of d(YGA) motifs. Our results show that the intercalation-locked tetraplex motif is predictable in these different sequence contexts and that substituting C⋅C base pairs for T⋅T base pairs introduces asymmetry to the homoduplex. These results have important implications for utilizing d(YGA) motifs in DNA crystal design and could provide a basis for understanding how local structures could be associated with repeat expansions. PMID:26629965

  19. Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

    PubMed Central

    Wenke, Belinda B.; Huiting, Leah N.; Frankel, Elisa B.; Lane, Benjamin F.; Núñez, Megan E.

    2014-01-01

    The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair Kop. In the normal duplex Kop decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a Kop of 8×10−7. In contrast, base pair opening at the 5’T of the thymine dimer is facile. The 5’T of the dimer has the largest equilibrium constant (Kop =3×10−4) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3’T of the dimer is much more stable than by the 5’T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5’ side more than on the 3’ side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions. PMID:24328089

  20. 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

  1. Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise.

    PubMed

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-05-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor of two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break. PMID:19420603

  2. Tunnel Conductance of Watson-Crick Nucleoside-Base Pairs from Telegraph Noise

    PubMed Central

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-01-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base-pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break. PMID:19420603

  3. On the internal d-wave structure of s+/- pairs in Iron-based Superconductors

    NASA Astrophysics Data System (ADS)

    Ong, Tze Tzen; Coleman, Piers

    2014-03-01

    A key issue in understanding the high temperature iron-based superconductors concerns the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. Whereas electronically paired superconductors generally avoid the Coulomb interaction through the formation of higher angular momentum pairs, iron based superconductors involve s-wave (s+/-) pairs with zero angular momentum. By taking account of the orbital degrees of freedom of the iron atoms, here we show that the s+/- pairs in these materials possess hidden d-wave symmetry, forming orbital triplets in which the the d-wave angular momentum of the pairs is compensated by the internal angular momentum of the orbitals. The recent observation of a gap with octahedral structure in KFe2As2 materials can be understood as a transition to a ``high spin'' configuration of the d-wave orbital triplets, through the alignment of the two angular momentum components of the pair. We acknowledge funding from DOE grant DE-FG02-99ER45790.

  4. 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. PMID:25967904

  5. 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).

  6. 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

  7. Isoalloxazine derivatives promote photocleavage of natural RNAs at G.U base pairs embedded within helices.

    PubMed Central

    Burgstaller, P; Hermann, T; Huber, C; Westhof, E; Famulok, M

    1997-01-01

    We have recently shown that isoalloxazine derivatives are able to photocleave RNA specifically at G.U base pairs embedded within a helical stack. The reaction involves the selective molecular recognition of G.U base pairs by the isoalloxazine ring and the removal of one nucleoside downstream of the uracil residue. Divalent metal ions are absolutely required for cleavage. Here we extend our studies to complex natural RNA molecules with known secondary and tertiary structures, such as tRNAs and a group I intron (td). G.U pairs were cleaved in accordance with the phylogenetically and experimentally derived secondary and tertiary structures. Tandem G.U pairs or certain G.U pairs located at a helix extremity were not affected. These new cleavage data, together with the RNA crystal structure, allowed us to perform molecular dynamics simulations to provide a structural basis for the observed specificity. We present a stable structural model for the ternary complex of the G. U-containing helical stack, the isoalloxazine molecule and a metal ion. This model provides significant new insight into several aspects of the cleavage phenomenon, mechanism and specificity for G. U pairs. Our study shows that in large natural RNAs a secondary structure motif made of an unusual base pair can be recognized and cleaved with high specificity by a low molecular weight molecule. This photocleavage reaction thus opens up the possibility of probing the accessibility of G.U base pairs, which are endowed with specific structural and functional roles in numerous structured and catalytic RNAs and interactions of RNA with proteins, in folded RNAs. PMID:9321652

  8. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.

    PubMed

    Zhou, Huiqing; Hintze, Bradley J; Kimsey, Isaac J; Sathyamoorthy, Bharathwaj; Yang, Shan; Richardson, Jane S; Al-Hashimi, Hashim M

    2015-04-20

    Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA. PMID:25813047

  9. Superconductivity, magnetism, and pairing symmetry in Fe-based superconductors

    NASA Astrophysics Data System (ADS)

    Eremin, Ilya

    2009-03-01

    We analyze antiferromagnetism and superconductivity within the renormalization group(RG) technique in novel Fe-based superconductors using the itinerant model of small electron and hole pockets near (0; 0) and (π,π), respectively, originating from the two strongly hybridized orbitals. We find that, for this model, the bare interactions in the Cooper channel are repulsive, and superconductivity does not occur at the mean-field level. However, under RG the effective interaction in the superconducting channel changes sign and becomes attractive. Furthermore, the effective interactions in antiferromagnetic and superconducting channels logarithmically flow towards the same absolute values at low energies, i.e., both must be treated on equal footings. The magnetic instability comes first for equal sizes of the two pockets, but looses to superconductivity upon doping. The superconducting gap has no nodes, but changes sign between the two Fermi surfaces (extended s-wave symmetry). We argue that the T dependencies of the spin susceptibility and NMR relaxation rate for such state are exponential only at very low T, and can be well fitted by power-laws over a wide T range below Tc. We further show that below Tc excitonic resonance appears in the spin excitations spectrum. [4pt] [1] M. Korshunov, and I. Eremin, Phys. Rev. B 78, 140509(R) (2008) [0pt] [2] A.V. Chubukov, D. Efremov, I. Eremin, Phys. Rev. B 78, 134512 (2008). [0pt] [3] M.M. Korshunov and I. Eremin, Europhys. Lett. 83, 67003 (2008).

  10. Charge transport in DNA oligonucleotides with various base-pairing patterns.

    PubMed

    Kratochvílová, Irena; Todorciuc, Tatiana; Král, Karel; Nemec, Hynek; Buncek, Martin; Sebera, Jakub; Zális, Stanislav; Vokácová, Zuzana; Sychrovský, Vladimír; Bednárová, Lucie; Mojzes, Peter; Schneider, Bohdan

    2010-04-22

    We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) and theoretical (density functional theory and molecular dynamics) approaches to study the relationships between the base-pairing patterns and the charge transfer properties in DNA 32-mer duplexes that may be relevant for identification and repair of defects in base pairing of the genetic DNA and for DNA use in nanotechnologies. Studied were two fully Watson-Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), and three with base pairs chemically removed. The results show that the charge transport varies strongly between these duplexes. The conductivity of the mismatched duplex is considerably lower than that of the W-C-paired one despite the fact that their structural integrities and thermal stabilities are comparable. Structurally and thermally much less stable abasic duplexes have still lower conductivity but not markedly different from the mismatched duplex. All duplexes are likely to conduct by the hole mechanism, and water orbitals increase the charge transport probability. PMID:20353252

  11. Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase iota.

    PubMed

    Johnson, Robert E; Prakash, Louise; Prakash, Satya

    2005-07-26

    Because of the near geometric identity of Watson-Crick (W-C) GxC and AxT base pairs, a given DNA polymerase forms the four possible correct base pairs with nearly identical catalytic efficiencies. However, human DNA polymerase iota (Pol iota), a member of the Y family of DNA polymerases, exhibits a marked template specificity, being more efficient at incorporating the correct nucleotide opposite template purines than opposite pyrimidines. By using 7-deazaadenine and 7-deazaguanine as the templating residues, which disrupt Hoogsteen base pair formation, we show that, unlike the other DNA polymerases belonging to the A, B, or Y family, DNA synthesis by Pol iota is severely inhibited by these N7-modified bases. These observations provide biochemical evidence that, during normal DNA synthesis, template purines adopt a syn conformation in the Pol iota active site, enabling the formation of a Hoogsteen base pair with the incoming pyrimidine nucleotide. Additionally, mutational studies with Leu-62, which lies in close proximity to the templating residue in the Pol iota ternary complex, have indicated that both factors, steric constraints within the active site and the stability provided by the hydrogen bonds in the Hoogsteen base pair, contribute to the efficiency of correct nucleotide incorporation opposite template purines by Pol iota. PMID:16014707

  12. 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

  13. 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

  14. Molecular mechanism of base pairing infidelity during DNA duplication upon one-electron oxidation

    PubMed Central

    Reynisson, Jóhannes

    2010-01-01

    The guanine radical cation (G•+) is formed by one-electron oxidation from its parent guanine (G). G•+ is rapidly deprotonated in the aqueous phase resulting in the formation of the neutral guanine radical [G(-H)•]. The loss of proton occurs at the N1 nitrogen, which is involved in the classical Watson-Crick base pairing with cytosine (C). Employing the density functional theory (DFT), it has been observed that a new shifted base pairing configuration is formed between G(-H)• and C constituting only two hydrogen bonds after deprotonation occurs. Using the DFT method, G(-H)• was paired with thymine (T), adenine (A) and G revealing substantial binding energies comparable to those of classical G-C and A-T base pairs. Hence, G(-H)• does not display any particular specificity for C compared to the other bases. Taking into account the long lifetime of the G(-H)• radical in the DNA helix (5 s) and the rapid duplication rate of DNA during mitosis/meiosis (5-500 bases per s), G(-H)• can pair promiscuously leading to errors in the duplication process. This scenario constitutes a new mechanism which explains how one-electron oxidation of the DNA double helix can lead to mutations. PMID:21603305

  15. Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate.

    PubMed

    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

  16. Premelting base pair opening probability and drug binding constant of a daunomycin-poly d(GCAT).poly d(ATGC) complex.

    PubMed Central

    Chen, Y Z; Prohofsky, E W

    1994-01-01

    We calculate room temperature thermal fluctuational base pair opening probability of a daunomycin-poly d(GCAT).poly d(ATGC) complex. This system is constructed at an atomic level of detail based on x-ray analysis of a crystal structure. The base pair opening probabilities are calculated from a modified self-consistent phonon approach of anharmonic lattice dynamics theory. We find that daunomycin binding substantially enhances the thermal stability of one of the base pairs adjacent the drug because of strong hydrogen bonding between the drug and the base. The possible effect of this enhanced stability on the drug inhibition of DNA transcription and replication is discussed. We also calculate the probability of drug dissociation from the helix based on the selfconsistent calculation of the probability of the disruption of drug-base H-bonds and the unstacking probability of the drug. The calculations can be used to determine the equilibrium drug binding constant which is found to be in good agreement with observations on similar daunomycin-DNA systems. PMID:8011914

  17. 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.

  18. 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.

  19. Tools for the automatic identification and classification of RNA base pairs

    PubMed Central

    Yang, Huanwang; Jossinet, Fabrice; Leontis, Neocles; Chen, Li; Westbrook, John; Berman, Helen; Westhof, Eric

    2003-01-01

    Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson–Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/. PMID:12824344

  20. 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.

  1. Formation of Silver Nanoclusters from a DNA Template Containing Ag(I)-Mediated Base Pairs

    PubMed Central

    Léon, J. Christian; Stegemann, Linda; Peterlechner, Martin; Litau, Stefanie; Wilde, Gerhard; Strassert, Cristian A.; Müller, Jens

    2016-01-01

    A series of DNA double helices containing different numbers of silver(I)-mediated base pairs involving the artificial nucleobases imidazole or 2-methylimidazole has been applied for the generation of DNA-templated silver nanoclusters. The original Ag(I)-containing nucleic acids as well as the resulting nanoclusters and nanoparticles have been characterized by means of UV/Vis spectroscopy, circular dichroism (CD) spectroscopy, fluorescence spectroscopy, and transmission electron microscopy (TEM). The results show for the first time that metal-mediated base pairs can be used for the templated growth of metal nanoclusters. PMID:27034627

  2. Discrimination of environmental background noise in presence of speech using sample-pairs statistics based features

    NASA Astrophysics Data System (ADS)

    Jhanwar, D.; Sharma, Kamlesh K.; Modani, S. G.

    2015-09-01

    A methodology to discriminate the different classes of background noise using new features based on samples of the signal is presented here. Two consecutive samples of different amplitude of the discretetime signals are termed as sample-pair and 14 types of sample-pairs are considered here as fundamental features. Results of simulation work proves that count of some of such type of sample-pairs as well as count of few combinations of two, three and four such sample-pairs are useful to detect and discriminate the different acoustic noise mixed with speech signals. On the basis of simulation results, the performance of proposed features have proved better than other spectral features like Mel Frequency Cepstral Coefficients (MFCC), Spectral Centroid, Spectral Flux and Spectral Roll-off regarding discrimination capabilities, simplicity of extraction process and lesser dependency over speech utterances mixed with noise. These sample-pairs based features having advantage of not requiring frame-decomposition and silence period removal. Their discrimination capabilities are shown by Fisher's F-ratio as performance index. The multiclass Support Vector Machine (SVM) is used as a classifier.

  3. 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

  4. Triple helical DNA in a duplex context and base pair opening

    PubMed Central

    Esguerra, Mauricio; Nilsson, Lennart; Villa, Alessandra

    2014-01-01

    It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson–Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson–Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region. PMID:25228466

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

    PubMed Central

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

    2010-01-01

    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

  6. 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.

  7. 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

  8. 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

  9. 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...

  10. 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

  11. 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

  12. 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.

  13. Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.

    PubMed

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-05-14

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition. PMID:12011426

  14. Looped out and perpendicular: Deformation of Watson–Crick base pair associated with actinomycin D binding

    PubMed Central

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-01-01

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5′-GXC/CYG-5′ complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson–Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition. PMID:12011426

  15. 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

  16. 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.

  17. The characteristics of gamma-prime dislocation pairs in a nickel-base superalloy

    NASA Technical Reports Server (NTRS)

    Gabb, T. P.; Miner, R. V.; Welsch, G.

    1987-01-01

    The gamma-prime dislocation pairs of a single crystal nickel-base superalloy, PWA 1480, after tensile and fatigue loading at 650 C are analyzed. The existence and extent of cube cross slip in octahedral slip, and the nature of gamma-prime dislocation pairs in primary cube slip are investigated. It is observed that the PWA 1480 specimens oriented near (001) and (-3 6 10) line directions deform by octahedral slip and specimens oriented near (-1 1 1) and (-2 3 4) lines deform by primary cube slip. It is determined that the overall dislocation distributions are more homogeneous in low cycle fatigue (LCF) loading than in monotonic tensile loading; however, the gamma-prime dislocation pair characteristics are similar for tensile and LCF test specimens. The data reveal that the gamma-prime dislocation pairs of octahedral slip specimens are near-screw and on the cube cross slip plane and for the cube slip specimens, the dislocation pairs are of various characters and on the primary cube slip plane.

  18. Nearest-neighbor parameters for 7-deaza-adenosine·uridine base pairs in RNA duplexes.

    PubMed

    Richardson, Katherine E; Znosko, Brent M

    2016-06-01

    One of the major limitations in RNA structure prediction is the lack of information about the effect of nonstandard nucleotides on stability. The nonstandard nucleotide 7-deaza-adenosine (7DA) is a naturally occurring analog of adenosine that has been studied for medicinal purposes and is commonly referred to as tubercidin. In 7DA, the nitrogen in the 7 position of adenosine is replaced by a carbon. Differences in RNA duplex stability due to the removal of this nitrogen can be attributed to a possible change in hydration and a difference in base stacking interactions resulting from changes in the electrostatics of the ring. In order to determine how 7DA affects the stability of RNA, optical melting experiments were conducted on RNA duplexes that contain either internal or terminal 7DA·U pairs with all possible nearest-neighbor combinations. On average, duplexes containing 7DA·U pairs are 0.43 and 0.07 kcal/mol less stable than what is predicted for the same duplex containing internal and terminal A-U pairs, respectively. Thermodynamic parameters for all nearest-neighbor combinations of 7DA·U pairs were derived from the data. These parameters can be used to more accurately predict the secondary structure and stability of RNA duplexes containing 7DA·U pairs. PMID:27099368

  19. Double proton transfer dynamics of model DNA base pairs in the condensed phase

    PubMed Central

    Kwon, Oh-Hoon; Zewail, Ahmed H.

    2007-01-01

    The dynamics of excited-state double proton transfer of model DNA base pairs, 7-azaindole dimers, is reported using femtosecond fluorescence spectroscopy. To elucidate the nature of the transfer in the condensed phase, here we examine variation of solvent polarity and viscosity, solute concentration, and isotopic fractionation. The rate of proton transfer is found to be significantly dependent on polarity and on the isotopic composition in the pair. Consistent with a stepwise mechanism, the results support the presence of an ionic intermediate species which forms on the femtosecond time scale and decays to the final tautomeric form on the picosecond time scale. We discuss the results in relation to the molecular motions involved and comment on recent claims of concerted transfer in the condensed phase. The nonconcerted mechanism is in agreement with previous isolated-molecule femtosecond dynamics and is also consistent with the most-recent high-level theoretical study on the same pair. PMID:17502610

  20. N-H stretching excitations in adenosine-thymidine base pairs in solution: pair geometries, infrared line shapes, and ultrafast vibrational dynamics.

    PubMed

    Greve, Christian; Preketes, Nicholas K; Fidder, Henk; Costard, Rene; Koeppe, Benjamin; Heisler, Ismael A; Mukamel, Shaul; Temps, Friedrich; Nibbering, Erik T J; Elsaesser, Thomas

    2013-01-24

    We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen configurations with similar probability. Steady-state concentration and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH(2) bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes. PMID:23234439

  1. Base-pairing promotes leader selection to prime in vitro influenza genome transcription.

    PubMed

    Geerts-Dimitriadou, Christina; Zwart, Mark P; Goldbach, Rob; Kormelink, Richard

    2011-01-01

    The requirements for alignment of capped leader sequences along the viral genome during influenza transcription initiation (cap-snatching) have long been an enigma. In this study, competition experiments using an in vitro transcription assay revealed that influenza virus transcriptase prefers leader sequences with base complementarity to the 3'-ultimate residues of the viral template, 10 or 11 nt from the 5' cap. Internal priming at the 3'-penultimate residue, as well as prime-and-realign was observed. The nucleotide identity immediately 5' of the base-pairing residues also affected cap donor usage. Application to the in vitro system of RNA molecules with increased base complementarity to the viral RNA template showed stronger reduction of globin RNA leader initiated influenza transcription compared to those with a single base-pairing possibility. Altogether the results indicated an optimal cap donor consensus sequence of (7m)G-(N)(7-8)-(A/U/G)-(A/U)-AGC-3'. PMID:21051068

  2. Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints

    PubMed Central

    2012-01-01

    Abstract A base-pairing probability matrix (BPPM) stores the probabilities for every possible base pair in an RNA sequence and has been used in many algorithms in RNA informatics (e.g., RNA secondary structure prediction and motif search). In this study, we propose a novel algorithm to perform iterative updates of a given BPPM, satisfying marginal probability constraints that are (approximately) given by recently developed biochemical experiments, such as SHAPE, PAR, and FragSeq. The method is easily implemented and is applicable to common models for RNA secondary structures, such as energy-based or machine-learning–based models. In this article, we focus mainly on the details of the algorithms, although preliminary computational experiments will also be presented. PMID:23210474

  3. 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.

  4. 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. PMID:26138135

  5. Evidence of competing s and d-wave pairing channels in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Kretzschmar, Florian; Muschler, Bernhard; Böhm, Thomas; Baum, Andreas; Hackl, Rudi; Wen, Hai-Hu; Tsurkan, Vladimir; Deisenhofer, Joachim; Loidl, Alois

    2013-03-01

    Superconductivity is determined by the interactions that drive Cooper pairing. However, experimental access to the pairing potential Vk ,k' becomes increasingly complicated upon going from conventional metals to complex systems such as the cuprates, some heavy fermion compounds or the iron-based superconductors. We show that electronic Raman scattering affords a window into the essential properties of Vk ,k' of iron-based superconductors. In Ba0 . 6K0 . 4Fe2As2 we observe band dependent energy gaps along with excitonic Bardasis-Schrieffer modes characterizing, respectively, the dominant and subdominant pairing channel. The dx2 -y2 symmetry of all excitons allows us to identify the subdominant channel to originate from the interaction between the electron bands. Consequently, the dominant channel driving superconductivity results from the interaction between the electron and hole bands and has the full lattice symmetry. The results in Rb0 . 8Fe1 . 6Se2 along with earlier ones in Ba(Fe0.939Co0 . 061) 2As2 highlight the influence of the Fermi surface topology on the pairing interactions.

  6. 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

  7. A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs

    NASA Astrophysics Data System (ADS)

    Shukla, P. K.; Ganapathy, Vinay; Mishra, P. C.

    2011-09-01

    Methylation of the DNA bases in the Watson-Crick GC and AT base pairs by the methyldiazonium ion was investigated employing density functional and second order Møller-Plesset (MP2) perturbation theories. Methylation at the N3, N7 and O6 sites of guanine, N1, N3 and N7 sites of adenine, O2 and N3 sites of cytosine and the O2 and O4 sites of thymine were considered. The computed reactivities for methylation follow the order N7(guanine) > N3(adenine) > O6(guanine) which is in agreement with experiment. The base pairing in DNA is found to play a significant role with regard to reactivities of the different sites.

  8. Theoretical investigation of the molecular structure of the pi kappa DNA base pair.

    PubMed

    Florián, J; Leszczyński, J

    1995-04-01

    The structure of the nonclassical pi kappa base pair (7-methyl-oxoformycin B. . .2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6-31G* and 6-31G** basis sets. The pi kappa base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition pattern. Recently, these bases were proposed as an extension of the genetic alphabet from four to six letters (Piccirilli et al, Nature 343,33 (1990)). By the HF/6-31G* method with full geometry optimization we calculated the 12 degree propeller twist for the minimum energy structure of this complex. The linearity of hydrogen bonds is preserved in the twisted structure by virtue of the pyramidal arrangement of the kappa-base amino groups. The rings of both the pi and kappa molecules remain nearly planar. This nonplanar structure of the pi kappa base pair is only 0.1 kcal/mol more stable than the planar (Cs) conformation. The HF/6-31G* level gas-phase interaction energy of pi kappa (-13.5 kcal/mol) calculated by us turned out to be nearly the same as the interaction energy obtained previously for the adenine-thymine base pair (-13.4 kcal/mol) at the same computational level. The inclusion of p-polarization functions on hydrogens, electron correlation effects (MP2/6-31G** level), and the correction for the basis set superposition error (BSSE) increase this energy to -14.0 kcal/mol. PMID:7626240

  9. DNA separation and fluorescent detection in an optofluidic chip with sub-base-pair resolution

    NASA Astrophysics Data System (ADS)

    Pollnau, Markus; Hammer, Manfred; Dongre, Chaitanya; Hoekstra, Hugo J.

    2015-03-01

    DNA sequencing in a lab-on-a-chip aims at providing cheap, high-speed analysis of low reagent volumes to, e.g., identify genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions/deletions from DNA fragments in the diagnostically relevant range of 150-1000 base-pairs requires a sizing accuracy of S < 10-3. Here we demonstrate S = 4×10-4. A microfluidic chip was post-processed by femtosecond-laser writing of an optical waveguide. 12 blue-labeled and 23 red-labeled DNA fragments were separated in size by capillary electrophoresis, each set excited by either of two lasers power-modulated at different frequencies, their fluorescence detected by a photomultiplier, and blue/red signals distinguished by Fourier analysis. Different calibration strategies were tested: a) use either set of DNA molecules as reference to calibrate the set-up and identify the base-pair sizes of the other set in the same flow experiment, thereby eliminating variations in temperature, wall-coating and sieving-gel conditions, and actuation voltages; b) use the same molecular set as reference and sample with the same fluorescence label, flown in consecutive experiments; c) perform cross-experiments based on different molecular sets with different labels, flown in consecutive experiments. From the results we conclude: Applying quadratic instead of linear fit functions improves the calibration accuracy. Blue-labeled molecules are separated with higher accuracy. The influence of dye label is higher than fluctuations between two experiments. Choosing a single, suitable dye label combined with reference calibration and sample investigation in consecutive experiments results in S = 4×10-4, enabling detection of single base-pair insertion/deletion in a lab-on-a-chip.

  10. Comparison of NIR FRET pairs for quantitative transferrin-based assay

    NASA Astrophysics Data System (ADS)

    Sinsuebphon, Nattawut; Bevington, Travis; Zhao, Lingling; Ken, Abe; Barroso, Margarida; Intes, Xavier

    2014-02-01

    Transferrin (Tfn) is commonly used as a drug delivery carrier for cancer treatment. Tfn cellular internalization can be observed by Förster resonance energy transfer (FRET), which occurs when two fluorophores - donor and acceptor - are a few nanometers apart. Donor fluorescence lifetime can be used to sense and quantify FRET occurrence. In FRET state, the donor is quenched leading to a significant reduction in its lifetime. In this study, donor and acceptor near-infrared (NIR) fluorophore-labeled Tfn were used to quantify cellular internalization in breast cancer cell line (T47D). Based on donor lifetime, quantum yield and spectral data, seven NIR FRET pairs were chosen for this comparison. Performance of the different NIR FRET pairs was evaluated in vitro in multiwell plate settings and by analyzing the relationship between quenched donor fraction and acceptor:donor ratio. Additionally, we performed brightness comparison between each pairs. Several parameters, such as brightness, lifetime, R0 and FRET donor population values are used to identify the most suitable NIR FRET pair for in vivo studies in preclinical settings.

  11. Modulation of Pairing Symmetry with Bond Disorder in Iron-based Superconductors

    NASA Astrophysics Data System (ADS)

    Yao, Dao-Xin; Kang, Yao-Tai; Tsai, Wei-Feng

    2015-03-01

    We study a simple two-orbital t-J1-J2 model for iron-based superconductors in the presence of a bond disorder (via nearest-neighbor bond-dilution). By using Bogoliubov-de Gennes approach, we self-consistently calculate the local pairing amplitudes and the corresponding density of states, which demonstrate a change of dominant pairing symmetry from the s+- wave to d-wave as long as J2 J1. Although the system exhibits spatially inhomogeneous pairing in weak correlations with a given realization of disorder, it is still in sharp contrast to the case with potential disorder, where the superconducting islands and the insulating sea are both present in the strong disorder regime. Moreover, from the detailed examination of the pairing gap as well as the superfluid density, the superconducting transition here is suggested to be beyond the conventional Abrikosov-Gorkov consideration. Supported by NBRPC-2012CB821400, NSFC-11074310, NSFC-11275279, Fundamental Research Funds for the Central Universities, and the NSC in Taiwan under Grant No.102-2112-M-110-009.

  12. 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

  13. 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.

  14. 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

  15. 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

  16. Low-energy electron scattering from DNA including structural water and base-pair irregularities

    SciTech Connect

    Caron, Laurent; Sanche, Leon; Tonzani, Stefano; Greene, Chris H.

    2009-07-15

    Elastic scattering of low-energy (0-13 eV) electrons from more realistic models of a DNA base-pair decamer is studied using multiple-scattering theory and T matrices obtained from ab initio R-matrix calculations. The models include two types of irregularities usually found in cellular DNA: base-pair mismatch and structural water molecules. Furthermore, we include in our calculation inelastic collisions. It is found that the basic interference patterns observed in the ideal and nonideal (i.e., more realistic) decamers are similar but have different amplitudes and are shifted in energy. Substantial inelastic losses, interestingly, cause pronounced local resonances, which could have an important influence in DNA strand breaks.

  17. Hydrogen bond disruption in DNA base pairs from (14)C transmutation.

    PubMed

    Sassi, Michel; Carter, Damien J; Uberuaga, Blas P; Stanek, Christopher R; Mancera, Ricardo L; Marks, Nigel A

    2014-09-01

    Recent ab initio molecular dynamics simulations have shown that radioactive carbon does not normally fragment DNA bases when it decays. Motivated by this finding, density functional theory and Bader analysis have been used to quantify the effect of C → N transmutation on hydrogen bonding in DNA base pairs. We find that (14)C decay has the potential to significantly alter hydrogen bonds in a variety of ways including direct proton shuttling (thymine and cytosine), thermally activated proton shuttling (guanine), and hydrogen bond breaking (cytosine). Transmutation substantially modifies both the absolute and relative strengths of the hydrogen bonding pattern, and in two instances (adenine and cytosine), the density at the critical point indicates development of mild covalent character. Since hydrogen bonding is an important component of Watson-Crick pairing, these (14)C-induced modifications, while infrequent, may trigger errors in DNA transcription and replication. PMID:25127298

  18. Single-Base Pair Genome Editing in Human Cells by Using Site-Specific Endonucleases

    PubMed Central

    Ochiai, Hiroshi

    2015-01-01

    Genome-wide association studies have identified numerous single-nucleotide polymorphisms (SNPs) associated with human diseases or phenotypes. However, causal relationships between most SNPs and the associated disease have not been established, owing to technical challenges such as unavailability of suitable cell lines. Recently, efficient editing of a single base pair in the genome was achieved using programmable site-specific nucleases. This technique enables experimental confirmation of the causality between SNPs and disease, and is potentially valuable in clinical applications. In this review, I introduce the molecular basis and describe examples of single-base pair editing in human cells. I also discuss the challenges associated with the technique, as well as possible solutions. PMID:26404258

  19. 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

  20. 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

  1. 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.

  2. Does base-pairing strength play a role in microRNA repression?

    PubMed

    Carmel, Ido; Shomron, Noam; Heifetz, Yael

    2012-11-01

    MicroRNAs (miRNAs) are short, single-stranded RNAs that silence gene expression by either degrading mRNA or repressing translation. Each miRNA regulates a specific set of mRNA "targets" by binding to complementary sequences in their 3' untranslated region. In this study, we examined the importance of the base-pairing strength of the miRNA-target duplex to repression. We hypothesized that if base-pairing strength affects the functionality of miRNA repression, organisms with higher body temperature or that live at higher temperatures will have miRNAs with higher G/C content so that the miRNA-target complex will remain stable. In the nine model organisms examined, we found a significant correlation between the average G/C content of miRNAs and physiological temperature, supporting our hypothesis. Next, for each organism examined, we compared the average G/C content of miRNAs that are conserved among distant organisms and that of miRNAs that are evolutionarily recent. We found that the average G/C content of ancient miRNAs is lower than recent miRNAs in homeotherms, whereas the trend was inversed in poikilotherms, suggesting that G/C content is associated with temperature, thus further supporting our hypothesis. In the organisms examined, the average G/C content of miRNA "seed" sequences was higher than that of mature miRNAs, which was higher than pre-miRNA loops, suggesting an association between the degree of functionality of the sequence and its average G/C content. Our analyses show a possible association between the base-pairing strength of miRNA-targets and the temperature of an organism, suggesting that base-pairing strength plays a role in repression by miRNAs. PMID:23019592

  3. Noncanonical registers and base pairs in human 5′ splice-site selection

    PubMed Central

    Tan, Jiazi; Ho, Jia Xin Jessie; Zhong, Zhensheng; Luo, Shufang; Chen, Gang; Roca, Xavier

    2016-01-01

    Accurate recognition of splice sites is essential for pre-messenger RNA splicing. Mammalian 5′ splice sites are mainly recognized by canonical base-pairing to the 5′ end of U1 small nuclear RNA, yet we described multiple noncanonical base-pairing registers by shifting base-pair positions or allowing one-nucleotide bulges. By systematic mutational and suppressor U1 analyses, we prove three registers involving asymmetric loops and show that two-nucleotide bulges but not longer can form in this context. Importantly, we established that a noncanonical uridine-pseudouridine interaction in the 5′ splice site/U1 helix contributes to the recognition of certain 5′ splice sites. Thermal melting experiments support the formation of noncanonical registers and uridine-pseudouridine interactions. Overall, we experimentally validated or discarded the majority of predicted noncanonical registers, to derive a list of 5′ splice sites using such alternative mechanisms that is much different from the original. This study allows not only the mechanistic understanding of the recognition of a wide diversity of mammalian 5′ splice sites, but also the future development of better splice-site scoring methods that reliably predict the effects of disease-causing mutations at these sequences. PMID:26969736

  4. Noncanonical registers and base pairs in human 5' splice-site selection.

    PubMed

    Tan, Jiazi; Ho, Jia Xin Jessie; Zhong, Zhensheng; Luo, Shufang; Chen, Gang; Roca, Xavier

    2016-05-01

    Accurate recognition of splice sites is essential for pre-messenger RNA splicing. Mammalian 5' splice sites are mainly recognized by canonical base-pairing to the 5' end of U1 small nuclear RNA, yet we described multiple noncanonical base-pairing registers by shifting base-pair positions or allowing one-nucleotide bulges. By systematic mutational and suppressor U1 analyses, we prove three registers involving asymmetric loops and show that two-nucleotide bulges but not longer can form in this context. Importantly, we established that a noncanonical uridine-pseudouridine interaction in the 5' splice site/U1 helix contributes to the recognition of certain 5' splice sites. Thermal melting experiments support the formation of noncanonical registers and uridine-pseudouridine interactions. Overall, we experimentally validated or discarded the majority of predicted noncanonical registers, to derive a list of 5' splice sites using such alternative mechanisms that is much different from the original. This study allows not only the mechanistic understanding of the recognition of a wide diversity of mammalian 5' splice sites, but also the future development of better splice-site scoring methods that reliably predict the effects of disease-causing mutations at these sequences. PMID:26969736

  5. 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’.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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. PMID:26933630

  11. 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

  12. 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.

  13. 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

  14. 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

  15. Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast.

    PubMed

    Gamble, Caitlin E; Brule, Christina E; Dean, Kimberly M; Fields, Stanley; Grayhack, Elizabeth J

    2016-07-28

    Translation elongation efficiency is largely thought of as the sum of decoding efficiencies for individual codons. Here, we find that adjacent codon pairs modulate translation efficiency. Deploying an approach in Saccharomyces cerevisiae that scored the expression of over 35,000 GFP variants in which three adjacent codons were randomized, we have identified 17 pairs of adjacent codons associated with reduced expression. For many pairs, codon order is obligatory for inhibition, implying a more complex interaction than a simple additive effect. Inhibition mediated by adjacent codons occurs during translation itself as GFP expression is restored by increased tRNA levels or by non-native tRNAs with exact-matching anticodons. Inhibition operates in endogenous genes, based on analysis of ribosome profiling data. Our findings suggest translation efficiency is modulated by an interplay between tRNAs at adjacent sites in the ribosome and that this concerted effect needs to be considered in predicting the functional consequences of codon choice. PMID:27374328

  16. Enhanced s +/- pairing due to prioritized diagonal motion of electrons in the iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Kuroki, Kazuhiko; Suzuki, Katsuhiro; Usui, Hidetomo

    2015-03-01

    In the itinerant spin picture of the iron-based superconductors, the nesting between electron and hole Fermi surfaces is usually considered to be the origin of the spin fluctuation. However, there are now some experimental results suggesting that the nesting is not important for superconductivity. An example is the 1111 materials LnFeAsO1-xHx (Ln=La,Sm etc.), where over 50% of electron doping can be accomplished. Superconductivity not only survives, but is even enhanced in the largely electron doped regime, in contradition to the expectation from the bad nesting. In LaFeAsO1-xHx in particular, the x vs. Tc phase diagram exhibits a double dome feature, suggesting a possible difference in the pairing mechanism between the lightly doped and the heavily doped regimes. In the present study, we analyze the five orbital model of this system, and show that a peculiar relation among the real space hoppings is realized in the largely electron doped regime, namely, the next nearest neighbor hopping dominates over the nearest one within the dxy orbitals. We argue that this enhances the s +/- pairing, which is a next nearest neighbor pairing in real space, despite the degraded nesting. We also discuss about some other materials having similar real space hoppings.

  17. 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.

  18. 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. PMID:27426255

  19. Ultrasound-driven preparation and pair distribution function-assisted structure solution of a copper-based layered coordination polymer.

    PubMed

    Mohideen, M Infas; Allan, Phoebe K; Chapman, Karena W; Hriljac, Joseph A; Morris, Russell E

    2014-07-21

    Nanoparticles of a copper-based layered coordination polymer, STAM-2, have been prepared via an ultrasound mediated transformation from a layered metal-organic framework, STAM-1. The structure of the material was then solved using pair distribution function analysis to identify the structural units present and the final structural model refined against the pair distribution function data. PMID:24310447

  20. Preonset studies of spondyloepiphyseal dysplasia tarda caused by a novel 2-base pair deletion in SEDL encoding sedlin.

    PubMed

    Mumm, S; Zhang, X; Gottesman, G S; McAlister, W H; Whyte, M P

    2001-12-01

    Spondyloepiphyseal dysplasia tarda (SEDT), an X-linked recessive skeletal disorder, presents with disproportionate short stature and "barrel-chest" deformity in affected (hemizygous) adolescent boys. In four reported families to date, mutations in a gene designated SEDL (spondyloepiphyseal dysplasia late) cosegregate with SEDT. We diagnosed SEDT in a short-stature, kyphotic 15-year-old boy because of his characteristic vertebral malformations. Clinical manifestations of SEDT were evident in at least four previous generations. A novel 2-base pair (bp) deletion in exon 5 of SEDL was found in the propositus by polymerase chain reaction (PCR) amplification and sequencing of all four coding exons. The mutation ATdel241-242 cosegregated with the kindred's skeletal disease. The deletion is adjacent to a noncanonical splice site for exon 5 but does not alter splicing. Instead, it deletes 2 bp from the coding sequence, causing a frameshift. A maternal aunt and her three young sons were investigated subsequently. Radiographs showed subtle shaping abnormalities of her pelvis and knees, suggesting heterozygosity. X-rays of the spine and pelvis of her 8-year-old son revealed characteristic changes of SEDT, but her younger sons (aged 6 years and 3 years) showed no abnormalities. SEDL analysis confirmed that she and only her eldest boy had the 2-bp deletion. Molecular testing of SEDL enables carrier detection and definitive diagnosis before clinical or radiographic expression of SEDT. Although there is no specific treatment for SEDT, preexpression molecular testing of SEDL could be helpful if avoiding physical activities potentially injurious to the spine and the joints proves beneficial. PMID:11760838

  1. Rearrangement or hydrogen-bonded ion pairs of protonated amines in solutions of bases

    SciTech Connect

    Nabiullin, A.A.; Mashkovskii, A.A.; Odinokov, S.E.

    1987-10-01

    Earlier the authors showed that the ion pairs of salts of protonated amines N/sup +/H...A/sup -/ (N/sup +/H is the triethylammonium, pyridinium, or 2,4,6-collidinium cation; A/sup -/ represents the anions SbCl/sub 6//sup -/, BF/sub 4//sup -/, ClO/sub 4//sup -/, I/sup -/) in binary or ternary (with inert solvent) solutions of bases are rearranged into ionic-molecular complexes (N/sup +/H...B) x A/sup -/. In these complexes the cation is bonded to a molecule of the solvating base by a H-bond N/sup +/H...B and to the anion by electrostatic forces, forming a contact ion pair. In this work, on the example of triethylammonium salts, they present the results of IR-spectroscopic investigations of the specific solvation by molecules of bases of systems in which the strength of the H-bond N/sup +/H...B is varied within wide limits. A large assortment of bases, from the weakest (nitromethane, acetonitrile) to the strongest (arsine and phosphine oxides, amines and their N-oxides), were used.

  2. 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

  3. Femtosecond decay dynamics of intact adenine and thymine base pairs in a supersonic jet.

    PubMed

    Kim, Nam Joon; Chang, Jinyoung; Kim, Hyung Min; Kang, Hyuk; Ahn, Tae Kyu; Heo, Jiyoung; Kim, Seong Keun

    2011-07-11

    We investigated the decay dynamics of the DNA base pairs adenine-adenine (A(2)), adenine-thymine (AT), and thymine-thymine (T(2)) produced in a supersonic jet by femtosecond (fs) time-resolved photoionization spectroscopy. The base pair was excited by a fs pump pulse at 267 nm and the population change of its excited state was monitored by non-resonant three-photon ionization using a fs probe pulse at 800 nm after a certain time delay. All of the transients recorded in the mass channel of the parent ion exhibited a tri-exponential decay, with time constants ranging from 100 fs to longer than 100 ps. Most of these time constants coincide well with the previous values deduced indirectly from the transients of protonated adenine (AH(+)) and thymine (TH(+)), which were assumed to be produced by fragmentation of the base-pair ions. Notably, for the transient of T(2), we observed a new decay component with a time constant of 2.3 ps, which was absent in the transient of TH(+). We suggest that the new decay component arises from the decay of stacked T(2) dimers that are mostly ionized to T(2)(+), whereas the decay signal recorded in the mass channel of TH(+) is merely from the relaxation of hydrogen-bonded T(2) dimers. From the amplitude of the new decay component, the population of the stacked T(2) dimers relative to the hydrogen-bonded dimers was estimated to be ∼2 % in the supersonic jet, which is about fifteen times higher than the theoretical value. PMID:21710523

  4. Ion Pair in Extreme Aqueous Environments, Molecular-Based and Electric Conductance Approaches

    SciTech Connect

    Chialvo, Ariel A; Gruszkiewicz, Miroslaw {Mirek} S; Simonson, J Michael {Mike}; Palmer, Donald; Cole, David R

    2009-01-01

    We determine by molecular-based simulation the density profiles of the Na+!Cl! ion-pair association constant in steam environments along three supercritical isotherms to interrogate the behavior of ion speciation in dilute aqueous solutions at extreme conditions. Moreover, we describe a new ultra-sensitive flow-through electric conductance apparatus designed to bridge the gap between the currently lowest steam-density conditions at which we are experimentally able to attain electric conductance measurements and the theoretically-reachable zero-density limit. Finally, we highlight important modeling challenges encountered near the zero-density limit and discuss ways to overcome them.

  5. 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.

  6. 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.

  7. 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.

  8. How Does Guanine-Cytosine Base Pair Affect Excess-Electron Transfer in DNA?

    PubMed

    Lin, Shih-Hsun; Fujitsuka, Mamoru; Majima, Tetsuro

    2015-06-25

    Charge transfer and proton transfer in DNA have attracted wide attention due to their relevance in biological processes and so on. Especially, excess-electron transfer (EET) in DNA has strong relation to DNA repair. However, our understanding on EET in DNA still remains limited. Herein, by using a strongly electron-donating photosensitizer, trimer of 3,4-ethylenedioxythiophene (3E), and an electron acceptor, diphenylacetylene (DPA), two series of functionalized DNA oligomers were synthesized for investigation of EET dynamics in DNA. The transient absorption measurements during femtosecond laser flash photolysis showed that guanine:cytosine (G:C) base pair affects EET dynamics in DNA by two possible mechanisms: the excess-electron quenching by proton transfer with the complementary G after formation of C(•-) and the EET hindrance by inserting a G:C base pair as a potential barrier in consecutive thymines (T's). In the present paper, we provided useful information based on the direct kinetic measurements, which allowed us to discuss EET through oligonucleotides for the investigation of DNA damage/repair. PMID:26042867

  9. 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

  10. Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

    PubMed Central

    Kondo, Jiro; Westhof, Eric

    2011-01-01

    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. PMID:21737431

  11. 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.

  12. 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

  13. How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations.

    PubMed Central

    Levitt, M

    1978-01-01

    Calculations on a 20-base pair segment of DNA double helix using empirical energy functions show that DNA can be bent smoothly and uniformly into a superhelix with a small enough radius (45 A) to fit the dimensions of chromatin. The variation of energy with the twist of the base pairs about the helix axis shows the straight DNA free in solution is most stable with about 10 1/2 base pairs per turn rather than 10 as observed in the solid state, whereas superhelical DNA in chromatin is most stable with about 10 base pairs per turn. This result, which has a simple physical interpretation, explains the pattern of nuclease cuts and the linkage number changes observed for DNA arranged in chromatin. PMID:273227

  14. Utility of a Computed Tomography-Based Navigation System (O-Arm) for En Bloc Partial Vertebrectomy for Lung Cancer Adjacent to the Thoracic Spine: Technical Case Report

    PubMed Central

    Kobayashi, Kazuyoshi; Ito, Zenya; Ando, Kei; Yokoi, Kohei; Ishiguro, Naoki

    2016-01-01

    We describe successful vertebrectomy from a posterior approach using a computed tomography (CT)-based navigation system (O-arm) in a 53-year-old man with adenocarcinoma of the posterior apex of the right lung with invasion of the adjacent rib, thoracic wall, and T2 and T3 vertebral bodies. En bloc partial vertebrectomy for lung cancer adjacent to the thoracic spine was planned using O-arm. First, laminectomy was performed from right T2 to T3, and pedicles and transverse processes of T2 to T3 were resected. O-arm was used to confirm the location of the cutting edge in the T2 to 3 right vertebral internal body, and osteotomy to the anterior cortex was performed with a chisel. Next, the patient was placed in a left decubitus position. The surgical specimen was extracted en bloc. This case shows that O-arm can be used reliably and easily in vertebrectomy from a posterior approach and can facilitate en bloc resection. PMID:27114780

  15. An efficient and near linear scaling pair natural orbital based local coupled cluster method

    NASA Astrophysics Data System (ADS)

    Riplinger, Christoph; Neese, Frank

    2013-01-01

    In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009), 10.1063/1.3173827]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 105-106 relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below <0.05%, which implies typically 15-20 but occasionally up to 30 atoms per domain on average. The new method has been given the acronym DLPNO-CCSD ("domain based LPNO-CCSD"). The method is nearly linear scaling with respect to system size. The original LPNO-CCSD method had three adjustable truncation thresholds that were chosen conservatively and do not need to be changed for actual applications. In the present treatment, no additional truncation parameters have been introduced. Any additional truncation

  16. 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

  17. 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.

  18. Identification of DNA lesions using a third base pair for amplification and nanopore sequencing

    PubMed Central

    Riedl, Jan; Ding, Yun; Fleming, Aaron M.; Burrows, Cynthia J.

    2015-01-01

    Damage to the genome is implicated in the progression of cancer and stress-induced diseases. DNA lesions exist in low levels, and cannot be amplified by standard PCR because they are frequently strong blocks to polymerases. Here, we describe a method for PCR amplification of lesion-containing DNA in which the site and identity could be marked, copied and sequenced. Critical for this method is installation of either the dNaM or d5SICS nucleotides at the lesion site after processing via the base excision repair process. These marker nucleotides constitute an unnatural base pair, allowing large quantities of marked DNA to be made by PCR amplification. Sanger sequencing confirms the potential for this method to locate lesions by marking, amplifying and sequencing a lesion in the KRAS gene. Detection using the α-hemolysin nanopore is also developed to analyse the markers in individual DNA strands with the potential to identify multiple lesions per strand. PMID:26542210

  19. 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.

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

    DOE PAGESBeta

    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

  1. 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

  2. Sheared-type G(anti).C(syn) base-pair: a unique d(GXC) loop closure motif.

    PubMed

    Chin, Ko-Hsin; Chou, Shan-Ho

    2003-05-30

    Stable DNA loop structures closed by a novel G.C base-pair have been determined for the single-residue d(GXC) loops (X=A, T, G or C) in low-salt solution by high-resolution nuclear magnetic resonance (NMR) techniques. The closing G.C base-pair in these loops is not of the canonical Watson-Crick type, but adopts instead a unique sheared-type (trans Watson-Crick/sugar-edge) pairing, like those occurring in the sheared mismatched G.A or A.C base-pair, to draw the two opposite strands together. The cytidine residue in the closing base-pair is transformed into the rare syn domain to form two H-bonds with the guanine base and to prevent the steric clash between the G 2NH(2) and the C H-5 protons. Besides, the sugar pucker of the syn cytidine is still located in the regular C2'-endo domain, unlike the C3'-endo domain adopted for the pyrimidines of the out-of-alternation left-handed Z-DNA structure. The facile formation of the compact d(GXC) loops closed by a unique sheared-type G(anti).C(syn) base-pair demonstrates the great potential of the single-stranded d(GXC) triplet repeats to fold into stable hairpins. PMID:12758081

  3. 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

  4. 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.

  5. 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.

  6. Ion-Pairing Assemblies Based on Pentacyano-Substituted Cyclopentadienide as a π-Electronic Anion.

    PubMed

    Bando, Yuya; Haketa, Yohei; Sakurai, Tsuneaki; Matsuda, Wakana; Seki, Shu; Takaya, Hikaru; Maeda, Hiromitsu

    2016-06-01

    Pentacyanocyclopentadienide (PCCp(-) ), a stable π-electronic anion, provided various ion-pairing assemblies in combination with various cations. PCCp(-) -based assemblies exist as single crystals and mesophases owing to interionic interactions with π-electronic and aliphatic cations with a variety of geometries, substituents, and electronic structures. Single-crystal X-ray analysis revealed that PCCp(-) formed cation-dependent arrangements with contributions from charge-by-charge and charge-segregated assembly modes for ion pairs with π-electronic and aliphatic cations, respectively. Furthermore, some aliphatic cations gave dimension-controlled organized structures with PCCp(-) , as observed in the mesophases, for which synchrotron XRD analysis suggested the formation of charge-segregated modes. Noncontact evaluation of conductivity for (C12 H25 )3 MeN(+) ⋅PCCp(-) films revealed potential hole-transporting properties, yielding a local-scale hole mobility of 0.4 cm(2)  V(-1)  s(-1) at semiconductor-insulator interfaces. PMID:27120581

  7. Extruded polymer films pigmented with a heterogeneous ion-pair based lumophore for O2 sensing.

    PubMed

    Mills, Andrew; Graham, Ashleigh

    2013-11-01

    A novel approach to polymeric Ru(II)-diimine luminescent O2 sensors is described. The Ru(II)-diimine, tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride ([Ru(dpp)3](2+)), is first ion-paired to the surface of heterogeneous TiO2 particles, rendered negatively charged due to the alkali nature of the aqueous solution, to produce an O2 sensitive pigment with a strikingly high oxygen sensitivity (i.e. PO2 (S = 1/2) = 0.002 atm, where PO2 (S = 1/2) is defined as the amount of oxygen required to reduce the initial, oxygen free luminescence by 50%), and a rapid response to oxygen. The pigment is extruded in low density polyethylene (LDPE) to produce a thin (60 μm), flexible, O2 sensing plastic film, with an O2 sensitivity (PO2 (S = 1/2) = 0.84 atm) comparable to the more traditional homogeneous lumophore ion-pair based O2 sensor ink films reported in the literature. PMID:24040643

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

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

    PubMed

    Fang, Wei; Chen, Ji; Rossi, Mariana; Feng, Yexin; Li, Xin-Zheng; Michaelides, Angelos

    2016-06-01

    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

  14. Pair normalized channel feature and statistics-based learning for high-performance pedestrian detection

    NASA Astrophysics Data System (ADS)

    Zeng, Bobo; Wang, Guijin; Ruan, Zhiwei; Lin, Xinggang; Meng, Long

    2012-07-01

    High-performance pedestrian detection with good accuracy and fast speed is an important yet challenging task in computer vision. We design a novel feature named pair normalized channel feature (PNCF), which simultaneously combines and normalizes two channel features in image channels, achieving a highly discriminative power and computational efficiency. PNCF applies to both gradient channels and color channels so that shape and appearance information are described and integrated in the same feature. To efficiently explore the formidably large PNCF feature space, we propose a statistics-based feature learning method to select a small number of potentially discriminative candidate features, which are fed into the boosting algorithm. In addition, channel compression and a hybrid pyramid are employed to speed up the multiscale detection. Experiments illustrate the effectiveness of PNCF and its learning method. Our proposed detector outperforms the state-of-the-art on several benchmark datasets in both detection accuracy and efficiency.

  15. 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.

  16. 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

  17. A 26-base-pair repetitive sequence specific for Neisseria gonorrhoeae and Neisseria meningitidis genomic DNA.

    PubMed Central

    Correia, F F; Inouye, S; Inouye, M

    1986-01-01

    Two-dimensional heteroduplex mapping of Neisseria gonorrhoeae genomic DNA revealed a number of spots, indicating the existence of repetitive sequences. When one of the spots was extracted and used as a probe for Southern blot analysis, two HindIII bands (11.0 and 3.6 kilobases [kb]) of the genomic digest hybridized with approximately equal intensity. The 3.6-kb fragment was cloned and found to contain two different types of repeated sequence. One type was approximately 1.1 kb in length and was found at least twice in the entire genome. The other consisted of a 26-base-pair family GT(C/A)C(Py)G(Pu)TTTTTGTTAAT(Py)C(Pu)CTATA (Py, pyrimidine; Pu, purine) that was repeated at least 20 times in the entire genome. This repetitive sequence was found also in Neisseria meningitidis but not in various other gram-negative bacteria. Images PMID:3091577

  18. 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

  19. 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. PMID:25741689

  20. Gapped graphene-based Josephson junction with d-wave pair coupling

    NASA Astrophysics Data System (ADS)

    Goudarzi, H.; Khezerlou, M.; Dezhaloud, T.

    2013-06-01

    The Josephson current passing through a S/I/S gapped graphene-based junction, where superconductivity in the S region is induced by depositing unconventional d-wave superconductor is investigated. The energy levels of massive Dirac fermions are exactly found for Andreev bound states. We illustrate the effect of characteristic of d-wave pairing symmetry on the Andreev bound states and the Josephson current. It is shown that the Josephson current vanishes for special range of superconductivity phase, φ = φ1 - φ2 and the position of the maximum current depends on the mass gap of graphene. The critical supercurrent varies in an oscillatory manner as function of the barrier strength, so that the period of oscillations does not change by increasing the effective mass of quasiparticles.

  1. 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.

  2. Hydrogen-bonding studies of amino acid side-chains with DNA base pairs

    NASA Astrophysics Data System (ADS)

    Deepa, P.; Kolandaivel, P.; Senthilkumar, K.

    2011-08-01

    The interactions of the amino acid side-chains arginine (ARG), aspartic acid (ASP), asparagine (ASN), lysine (LYS) and serine (SER) with nucleic acid base pairs have been investigated using theoretical methods. The interaction energy of the short intermolecular N-H ... N, N-H ... O, O-H ... O, O-H ... N, C-H ... O and C-H ... N hydrogen bonds present in both isolated base pairs and complexes and its role in providing stability to the complexes have been explored. The homonuclear interactions are found to be stronger than the heteronuclear interactions. An improper hydrogen bond has been observed for some of the N-H ... O and N-H ... N hydrogen-bond interactions with the contraction of the N-H bond varying from 0.001 to 0.0260 Å and the corresponding blue shift of the stretching frequency by 4-291 cm-1. Localized molecular orbital energy decomposition analysis (LMOEDA) reveals that the major contributions to the energetics are from the long-range polarization (PL) interaction, and the short-range attractive (ES, EX) and repulsive (REP) interactions. The Bader's atoms in molecules (AIM) theory shows good correlation for the electron density and its Laplacian at the bond critical points (BCP) with the N-H ... N and N-H ... O hydrogen-bond lengths in the complexes, and gives a proper explanation for the stability of the structure. The charge-transfer from the proton acceptor to the antibonding orbital of the X-H bond in the complexes was studied using natural bond orbital (NBO) analysis.

  3. Genetic association mapping based on discordant sib pairs: the discordant-alleles test.

    PubMed

    Boehnke, M; Langefeld, C D

    1998-04-01

    Family-based tests of association provide the opportunity to test for an association between a disease and a genetic marker. Such tests avoid false-positive results produced by population stratification, so that evidence for association may be interpreted as evidence for linkage or causation. Several methods that use family-based controls have been proposed, including the haplotype relative risk, the transmission-disequilibrium test, and affected family-based controls. However, because these methods require genotypes on affected individuals and their parents, they are not ideally suited to the study of late-onset diseases. In this paper, we develop several family-based tests of association that use discordant sib pairs (DSPs) in which one sib is affected with a disease and the other sib is not. These tests are based on statistics that compare counts of alleles or genotypes or that test for symmetry in tables of alleles or genotypes. We describe the use of a permutation framework to assess the significance of these statistics. These DSP-based tests provide the same general advantages as parent-offspring trio-based tests, while being applicable to essentially any disease; they may also be tailored to particular hypotheses regarding the genetic model. We compare the statistical properties of our DSP-based tests by computer simulation and illustrate their use with an application to Alzheimer disease and the apolipoprotein E polymorphism. Our results suggest that the discordant-alleles test, which compares the numbers of nonmatching alleles in DSPs, is the most powerful of the tests we considered, for a wide class of disease models and marker types. Finally, we discuss advantages and disadvantages of the DSP design for genetic association mapping. PMID:9529345

  4. 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

  5. In silico studies toward understanding the interactions of DNA base pairs with protonated linear/cyclic diamines.

    PubMed

    Sen, Anik; Sahu, Debashis; Ganguly, Bishwajit

    2013-08-29

    Protonated amino groups are ubiquitous in nature and important in the fields of chemistry and biology. In search of efficient polyamine analogues, we have performed DFT calculations on the interactions of some simple cyclic and constrained protonated diamines with the DNA base pairs and compared the results with those obtained for the corresponding interactions involving linear diamines, which mimic biogenic polyamines such as spermine. The interactions are mainly governed by the strong hydrogen bonding between the ligand and the DNA base pairs. The DFT calculations suggest that the major-groove N7 interaction (GC base pair) with linear diamine is energetically more favored than other possible interactions, as reported with spermine. The cyclic diamines exhibited better interactions with the N7 site of the AT and GC base pairs of DNA than the linear diamines. The net atomic charges calculated for the protonated amine hydrogens were higher for the cyclic systems than for the linear diamines, inducing better binding affinity with the DNA base pairs. The stable conformers of cyclic diamines were predicted using the MP2/aug-cc-pVDZ level of theory. The positions of the protonated diamine groups in these cyclic systems are crucial for effective binding with the DNA base pairs. The DFT-calculated results show that diequatorial (ee) 1,2-cyclohexadiamine (CHDA) is a promising candidate as a polyamine analogue for biogenic polyamines. Molecular dynamics simulations were performed using explicit water molecules for the interaction of representative ligands with the DNA base pairs to examine the influence of solvent molecules on such interactions. PMID:23909683

  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. miRNA-dis: microRNA precursor identification based on distance structure status pairs.

    PubMed

    Liu, Bin; Fang, Longyun; Chen, Junjie; Liu, Fule; Wang, Xiaolong

    2015-04-01

    MicroRNA precursor identification is an important task in bioinformatics. Support Vector Machine (SVM) is one of the most effective machine learning methods used in this field. The performance of SVM-based methods depends on the vector representations of RNAs. However, the discriminative power of the existing feature vectors is limited, and many methods lack an interpretable model for analysis of characteristic sequence features. Prior studies have demonstrated that sequence or structure order effects were relevant for discrimination, but little work has explored how to use this kind of information for human pre-microRNA identification. In this study, in order to incorporate the structure-order information into the prediction, a method called "miRNA-dis" was proposed, in which the feature vector was constructed by the occurrence frequency of the "distance structure status pair" or just the "distance-pair". Rigorous cross-validations on a much larger and more stringent newly constructed benchmark dataset showed that the miRNA-dis outperformed some state-of-the-art predictors in this area. Remarkably, miRNA-dis trained with human data can correctly predict 87.02% of the 4022 pre-miRNAs from 11 different species ranging from animals, plants and viruses. miRNA-dis would be a useful high throughput tool for large-scale analysis of microRNA precursors. In addition, the learnt model can be easily analyzed in terms of discriminative features, and some interesting patterns were discovered, which could reflect the characteristics of microRNAs. A user-friendly web-server of miRNA-dis was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/miRNA-dis/. PMID:25715848

  8. 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.

  9. 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

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

    PubMed Central

    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

  11. A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin.

    PubMed Central

    Coll, M; Frederick, C A; Wang, A H; Rich, A

    1987-01-01

    The crystal structures of d(CGCA3T3GCG) complex to the antitumor drug distamycin and the DNA fragment alone were solved by x-ray diffraction at 2.2 and 2.5 A resolution, respectively. The drug lies in the narrow minor groove near the center of the B-DNA fragment covering 5 of the 6 A.T base pairs. It is bound to the DNA by hydrogen bonding, van der Waals, and electrostatic interactions. In addition, the DNA was found to have an unusual conformation in the (dA)3.(dT)3 regions. These base pairs have a high positive propeller twist so that in the major groove the adenine amino group is located intermediate between the carbonyl O-4 groups of two adjacent thymines of the opposite strand, making bifurcated hydrogen bonds to the two thymine residues. This suggests a model to explain the unusual properties of poly-(dA).poly(dT) in which a modified B conformation is associated with a large propeller twist of the bases and a set of continuous bifurcating hydrogen bonds along the major groove, which may provide incremental stability to these segments. In addition, shorter segments of (dA)3-6.(dT)3-6 may have this conformation in the midst of B-DNA and stabilize bends in the DNA that may be associated with stacking on one of the high propeller-twisted bases at the ends of these segments. Images PMID:3479798

  12. Future hospital care in a population-based series of twin pairs discordant for physical activity behavior.

    PubMed Central

    Kujala, U M; Kaprio, J; Sarna, S; Koskenvuo, M

    1999-01-01

    OBJECTIVES: This study investigated the association between physical activity behavior and morbidity, taking into account genetic selection. METHODS: Hospitalizations were followed from the beginning of 1977 to the end of 1986 in 710 same-sex healthy twin pairs discordant for leisure-time physical activity and in 151 pairs discordant for all physical activity at base-line in 1975. RESULTS: During the follow-up, among twin pairs discordant for leisure activity, the active member spent, on average, 43% fewer days in the hospital than the inactive member; the corresponding percentage was 55% among pairs discordant for all activity. CONCLUSIONS: Physically inactive behavior is associated with increased need for hospital treatments, even after genetic and other confounding factors are taken into account. PMID:10589321

  13. Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs.

    PubMed

    Mondal, Manas; Halder, Sukanya; Chakrabarti, Jaydeb; Bhattacharyya, Dhananjay

    2016-04-01

    Stacking interaction between the aromatic heterocyclic bases plays an important role in the double helical structures of nucleic acids. Considering the base as rigid body, there are total of 18 degrees of freedom of a dinucleotide step. Some of these parameters show sequence preferences, indicating that the detailed atomic interactions are important in the stacking. Large variants of non-canonical base pairs have been seen in the crystallographic structures of RNA. However, their stacking preferences are not thoroughly deciphered yet from experimental results. The current theoretical approaches use either the rigid body degrees of freedom where the atomic information are lost or computationally expensive all atom simulations. We have used a hybrid simulation approach incorporating Monte-Carlo Metropolis sampling in the hyperspace of 18 stacking parameters where the interaction energies using AMBER-parm99bsc0 and CHARMM-36 force-fields were calculated from atomic positions. We have also performed stacking energy calculations for structures from Monte-Carlo ensemble by Dispersion corrected density functional theory. The available experimental data with Watson-Crick base pairs are compared to establish the validity of the method. Stacking interaction involving A:U and G:C base pairs with non-canonical G:U base pairs also were calculated and showed that these structures were also sequence dependent. This approach could be useful to generate multiscale modeling of nucleic acids in terms of coarse-grained parameters where the atomic interactions are preserved. This method would also be useful to predict structure and dynamics of different base pair steps containing non Watson-Crick base pairs, as found often in the non-coding RNA structures. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 212-226, 2016. PMID:26600167

  14. Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs.

    PubMed Central

    Coll, M; Fita, I; Lloveras, J; Subirana, J A; Bardella, F; Huynh-Dinh, T; Igolen, J

    1988-01-01

    The left-handed Z-DNA conformation has been observed in crystals made from the self-complementary DNA hexamer d(CACGTG). This is the first time that a non disordered Z form is found in the crystal structure of an alternating sequence containing AT base pairs without methylated or brominated cytosines. The structure has been determined and refined to an agreement factor R = 22.9% using 746 reflections in the resolution in the resolution shell 7 to 2.5 A. The overall shape of the molecule is very similar to the Z-structure of the related hexamer d(CG)3 confirming the rigidity of the Z form. No solvent molecules were detected in the minor groove of the helix near the A bases. The disruption of the spine of hydration in the AT step appears to be a general fact in the Z form in contrast with the B form. The biological relevance of the structure in relation to the CA genome repeats is discussed. PMID:3419929

  15. 2',4'-BNA bearing a 2-pyridine nucleobase for CG base pair recognition in the parallel motif triplex DNA.

    PubMed

    Hari, Yoshiyuki; Matsugu, Sachiko; Inohara, Hiroyasu; Hatanaka, Yuri; Akabane, Masaaki; Imanishi, Takeshi; Obika, Satoshi

    2010-09-21

    We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2',4'-BNA congener (Py(B)). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recognition of a CG base pair within double-stranded DNA (dsDNA) in a parallel motif triplex. Moreover, Py(B) in TFOs showed stronger affinity to a CG base pair than Py with further increase in the selectivity. Using TFO including multiple Py(B) units, triplex formation with dsDNA containing three CG base pairs was observed. PMID:20648389

  16. Evidence for tautomerism in nucleic acid base pairs. 1H NMR study of 15N labeled tRNA.

    PubMed Central

    Rüterjans, H; Kaun, E; Hull, W E; Limbach, H H

    1982-01-01

    The imino proton resonances of 15N labeled tRNA appear as asymmetric doublet signals, the asymmetry being dependent on the applied magnetic field strength. Assuming a tautomerism of the type N-H...N not equal to N...H-N in the base pairs the line shapes can be simulated. The most important parameters fitted in the simulation are the rate constants of the proton transfer and the mole fractions of either tautomeric state. The rate constants are of the order of 100s-1 and the mole fractions of the non dominant tautomer about 0.1 depending on the temperature and on the nature of the base pairing. The observations are attributed to a double proton transfer in the base pairs. The unexpectedly slow rates of the double proton transfer process may be connected with a concomitant conformational change of the duplex structure. PMID:7177856

  17. 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

  18. 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.

  19. Base pairing enhances fluorescence and favors cyclobutane dimer formation induced upon absorption of UVA radiation by DNA.

    PubMed

    Banyasz, Akos; Vayá, Ignacio; Changenet-Barret, Pascale; Gustavsson, Thomas; Douki, Thierry; Markovitsi, Dimitra

    2011-04-13

    The photochemical properties of the DNA duplex (dA)(20)·(dT)(20) are compared with those of the parent single strands. It is shown that base pairing increases the probability of absorbing UVA photons, probably due to the formation of charge-transfer states. UVA excitation induces fluorescence peaking at ∼420 nm and decaying on the nanosecond time scale. The fluorescence quantum yield, the fluorescence lifetime, and the quantum yield for cyclobutane dimer formation increase upon base pairing. Such behavior contrasts with that of the UVC-induced processes. PMID:21417388

  20. A 145-base pair DNA sequence that positions itself precisely and asymmetrically on the nucleosome core.

    PubMed Central

    Ramsay, N; Felsenfeld, G; Rushton, B M; McGhee, J D

    1984-01-01

    A 145-bp DNA sequence, cloned from Escherichia coli, was reconstituted into nucleosome core particles by a number of methods. The behaviour of the resulting complex upon sucrose gradient sedimentation and nucleoprotein gel electrophoresis closely resembled that of control bulk nucleosome core particles. DNase I digestion of the 32P-end-labelled complex revealed the 10-bp periodicity of cleavages expected for DNA bound on a histone surface. The narrow cleavage sites observed (1 bp wide) imply that the sequence occupies a single preferred position on the nucleosome core, accurate to the level of single base pairs. By relating the digestion pattern observed to the pattern of site protection found for random sequence nucleosomes, the DNA position was found to be offset by 17 bp from that in the normal core particle. A number of experiments argue against the involvement of length or end effects and suggest that it is some feature of the DNA sequence itself that determines this precise positioning of DNA on the nucleosome. Images Fig. 3. Fig. 4. Fig. 5. PMID:6096135

  1. 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

  2. Locations of Joint Physical Activity in Parent-Child Pairs Based on Accelerometer and GPS Monitoring

    PubMed Central

    Dunton, Genevieve Fridlund; Liao, Yue; Almanza, Estela; Jerrett, Micheal; Spruijt-Metz, Donna; Pentz, Mary Ann

    2012-01-01

    Background Parental factors may play an important role in influencing children’s physical activity levels. Purpose This cross-sectional study sought to describe the locations of joint physical activity among parents and children. Methods Parent-child pairs (N = 291) wore an Actigraph GT2M accelerometer and GlobalSat BT-335 Global Positioning Systems (GPS) device over the same 7-day period. Children were ages 8–14 years. Joint behavior was defined by a linear separation distance of less than 50m between parent and child. Land use classifications were assigned to GPS data points. Results Joint physical activity was spread across residential locations (35%), and commercial venues (24%), and open spaces/parks (20%). Obese children and parents performed less joint physical activity in open spaces/parks than under/normal weight children and parents (p’s < .01). Conclusions Understanding where joint parent-child physical activity naturally occurs may inform location-based interventions to promote these behaviors. PMID:23011914

  3. 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

  4. Biomolecule Analogues 2-Hydroxypyridine and 2-Pyridone Base Pairing on Ice Nanoparticles.

    PubMed

    Rubovič, Peter; Pysanenko, Andriy; Lengyel, Jozef; Nachtigallová, Dana; Fárník, Michal

    2016-07-14

    Ice nanoparticles (H2O)N, N ≈ 450 generated in a molecular beam experiment pick up individual gas phase molecules of 2-hydroxypyridine and 2-pyridone (HP) evaporated in a pickup cell at temperatures between 298 and 343 K. The mass spectra of the doped nanoparticles show evidence for generation of clusters of adsorbed molecules (HP)n up to n = 8. The clusters are ionized either by 70 eV electrons or by two photons at 315 nm (3.94 eV). The two ionization methods yield different spectra, and their comparison provides an insight into the neutral cluster composition, ionization and intracluster ion-molecule reactions, and cluster fragmentation. Quite a few molecules were reported not to coagulate on ice nanoparticles previously. The (HP)n cluster generation on ice nanoparticles represents the first evidence for coagulating of molecules and cluster formation on free ice nanoparticles. For comparison, we investigate the coagulation of HP molecules picked up on large clusters ArN, N ≈ 205, and also (HP)n clusters generated in supersonic expansions with Ar buffer gas. This comparison points to a propensity for the (HP)2 dimer generation on ice nanoparticles. This shows the feasibility of base pairing for model of biological molecules on free ice nanoparticles. This result is important for hypotheses of the biomolecule synthesis on ice grains in the space. We support our findings by theoretical calculations that show, among others, the HP dimer structures on water clusters. PMID:26785038

  5. 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.

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

    PubMed Central

    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. PMID:27190534

  7. Doppler Broadening Analysis of Steel Specimens Using Accelerator Based In Situ Pair Production

    SciTech Connect

    Makarashvili, V.; Wells, D. P.; Roy, A. K.

    2009-03-10

    Positron Annihilation Spectroscopy (PAS) techniques can be utilized as a sensitive probe of defects in materials. Studying these microscopic defects is very important for a number of industries in order to predict material failure or structural integrity. We have been developing gamma-induced pair-production techniques to produce positrons in thick samples ({approx}4-40 g/cm{sup 2}, or {approx}0.5-5 cm in steel). These techniques are called 'Accelerator-based Gamma-induced Positron Annihilation Spectroscopy'(AG-PAS). We have begun testing the capabilities of this technique for imaging of defect densities in thick structural materials. As a first step, a linear accelerator (LINAC) was employed to produce photon beams by stopping 15 MeV electrons in a 1 mm thick tungsten converter. The accelerator is capable of operating with 30-60 ns pulse width, up to 200 mA peak current at 1 kHz repetition rate. The highly collimated bremsstrahlung beam impinged upon our steel tensile specimens, after traveling through a 1.2 m thick concrete wall. Annihilation radiation was detected by a well-shielded and collimated high-purity germanium detector (HPGe). Conventional Doppler broadening spectrometry (DBS) was performed to determine S, W and T parameters for our samples.

  8. 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.

  9. Decentralized supervisory based switching control for uncertain multivariable plants with variable input-output pairing.

    PubMed

    Namaki-Shoushtari, Omid; Khaki-Sedigh, Ali

    2012-01-01

    In this paper, the design of decentralized switching control for uncertain multivariable plants is considered. In the proposed strategy, the uncertainty region is divided into smaller regions with a nominal model and specific control structure. The underlying design is based on the quantitative feedback theory (QFT). It is assumed that a MIMO-QFT controller exists for robust stability and performance of the individual uncertain sets. The proposed control structure is made up by these local decentralized controllers, which commute among themselves in accordance with the decision of a high level decision maker called the supervisor. The supervisor makes the decision by comparing the local models' behaviors with the one of the plant and selects the controller corresponding to the best fitted model. A hysteresis switching logic is used to slow down the switching to guarantee the overall closed loop stability. It is shown that this strategy provides a stable and robust adaptive controller to deal with complex multivariable plants with input-output pairing changes during the plant operation, which can facilitate the development of a reconfigurable decentralized control. Also, the multirealization technique is used to implement a family of controllers to achieve bumpless transfer. Simulation results are employed to show the effectiveness of the proposed method. PMID:21999896

  10. Enhanced spin fluctuations and s +/- pairing by diagonal electron hopping in Fe-based superconductors

    NASA Astrophysics Data System (ADS)

    Kuroki, Kazuhiko

    2015-03-01

    In the itinerant spin picture of the iron-based superconductors, the nesting between electron and hole Fermi surfaces is usually considered to be the origin of the spin fluctuation and thus the pairing glue. However, there have appeared some experimental observations suggesting absence of Fermi surface nesting. For instance, in the 1111 materials Ln FeAsO1-xHx (Ln =La,Sm, etc.), electron doping rate x reaches up to 50%, which in a rigid band picture would wipe out the hole Fermi surfaces. Still, superconductivity not only survives, but is even enhanced in the largely doped regime, in contradiction to the expectation from the bad nesting. Another example is KxFe2-ySe2, where the ARPES experiments show the absence of hole Fermi surfaces. In the present talk, we first focus on Ln FeAsO1-xHx, where the band structure is actually not rigid against doping, and the hole Fermi surface originating from the dxy orbital remains nearly unchanged. The origin of this can be traced back to real space, where the nearest neighbor hopping t1 within the dxy orbital is found to be strongly suppressed with doping. Although the nesting itself is degraded, the spin fluctuation in the largely electron doped regime is enhanced due to t2 >t1 , where t2 is the 2nd neighbor diagonal hopping. This re-enhances s +/- pairing superconductivity, and explains the double dome x-Tc phase diagram of LaFeAsO1-xHx. From this viewpoint, it is also interesting to look into the relation between t1 and t2 in other materials. For instance, our first principles estimation for KFe2Se2givest1 = - 0 . 008 eV and t2 = 0 . 056 eV, and from this strong reduction of t1, both electron and hole Fermi surfaces are expected to be present around the Γ point, in contradiction to previous experimental observations. Results of a recent ARPES experiment will be discussed from this viewpoint.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. [Structural and energetic properties of the four configurations of the A.T and G.C DNA base pairs].

    PubMed

    Brovarets', O O

    2013-01-01

    Using the methods of non-empirical quantum chemistry at the MP2/6-311++G(2df,pd)// B3LYP/6-311++G(d,p) level of theory it was established for the first time, that Hoogsteen, reverse Hoogsteen, Watson-Crick and reverse Watson-Crick configurations of the A.T and G.C DNA base pairs are isoelectronic and isomorphic structures with similar dynamic properties. Based on these results, non-ionisation mechanism of the Hoogsteen <"breathing" of the G*.C* DNA base pair, namely transformation of the tautomerised (Lowdin's) G-C base pair with Watson-Crick geometry into the Hoogsteen electroneutral G*.C* H base pair stabilized by the three O6H...N4, N3H...N7 and C8H...02 H-bonds, was postulated. It is suggested that such scenario activates only in those cases, when DNA is not located in aqueous solution, but works together with proteins and cytosine protonation at the N3 atom is precluded. PMID:24319980

  17. Role of interaction energy in the specificity of transcription. I-The Watson Crick G-C base pair template.

    PubMed Central

    Sanyal, N K; Kumar, U; Roychoudhury, M

    1980-01-01

    The purpose of this work is to show that the selectivity of the nucleotide bases in RNA transcription c an be inferred, in principle, from the DNA base pair - RNA base interaction. The catalytic role of enzymes in this process is, therefore, only to form the sugar - phosphate backbone. A systematic study for the evaluation of the interaction energy of the DNA base pair with the enterant RNA bases have been undertaken to elucidate the aforesaid mechanism. Electrostatic hard sphere approximation of Nash and Bradley 1 has been employed. Non bonded induced dipole and London dispersion forces are not taken into account. The present communication gives the results of computations of the interaction energy of the four RNA bases. The results have been discussed with reference to Stent's and Zubay's schemes of RNA transcription. PMID:7443519

  18. Ultrafast IR pump-probe and 2D-IR photon echo spectroscopy of adenosine-thymidine base pairs

    NASA Astrophysics Data System (ADS)

    Greve, Christian; Preketes, Nicholas K.; Costard, Rene.; Koeppe, Benjamin; Fidder, Henk; Nibbering, Erik T. J.; Temps, Friedrich; Mukamel, Shaul; Elsaesser, Thomas

    2013-03-01

    We characterize diagonal and off-diagonal anharmonicities of N-H stretching vibrations in adenosine and thymidine monomers and in A•T-base pairs in chloroform solution, showing the important role of coupling between vibrationally excited N-H stretching states.

  19. 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 ...

  20. Lewis base activation of borane-dimethylsulfide into strongly reducing ion pairs for the transformation of carbon dioxide to methoxyboranes.

    PubMed

    Légaré, Marc-André; Courtemanche, Marc-André; Fontaine, Frédéric-Georges

    2014-10-01

    The hydroboration of carbon dioxide into methoxyboranes by borane-dimethylsulfide using different base catalysts is described. A non-nucleophilic proton sponge is found to be the most active catalyst, with TOF reaching 64 h(-1) at 80 °C, and is acting via the activation of BH3·SMe2 into a boronium-borohydride ion pair. PMID:25164269

  1. 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

  2. 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.

  3. 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

  4. Fast Reconnection Rates Based on Group Velocity Cones: Whistler Regime and Pair Plasmas

    NASA Astrophysics Data System (ADS)

    Singh, N.

    2009-05-01

    Based on the group velocity vector of the whistler mode, we predict the range of whistler-regime reconnection rate depending on the half width (w) of the current sheet (CS. During the reconnection process electromagnetic perturbations (EMPs) are generated in the localized diffusion region (DR, which acts like an antenna and radiates whistler waves for certain range of CS widths. The reconnection structure (exhaust) is approximately the radiation pattern of the DR antenna and it is determined by the group velocity directions. Since the whistler waves originate from the electromagnetic perturbations (EMPs) localized in the DR, we calculate R over a range of the discrete values of the perpendicular wave number (k'') contained in the Fourier spectrum of the EMPs. We have used such calculations to determine the reconnection rates averaged over the wave number spectrum of a Gaussian shaped EMP as a function of the CS width. We find that has a fairly constant value at ˜ 0.23 for CS widths in the range 0.4 < w/di ˜ 1 and for w < 0.3di it decreases with decreasing w and it attains a value ˜ 0.06 in an extremely thin CS with w ˜ 0.05di, where di is the ion skin depth. We compare the values of and R with those found from simulations and experiments, and find them in good agreement. We also report the properties of the whistler waves radiated from the DR into the exhaust region. We also demonstrate that our theoretical method developed for whistler regime reconnection could be easily adopted to predict fast reconnection rates in pair plasmas, which support inertial Alfven waves.

  5. Relationship between pairing symmetries and interaction parameters in iron-based superconductors from functional renormalization group calculations

    NASA Astrophysics Data System (ADS)

    Yuan, Jing; Hu, Jiangping

    2016-03-01

    Pairing symmetries of iron-based superconductors are investigated systematically in a five-orbital model within the different regions of interaction parameters by functional renormalization group (FRG). Even for a fixed Fermi surface with both hole and electron pockets, it is found that depending on interaction parameters, a variety of pairing symmetries, including two types of d-wave and two types of s-wave pairing symmetries, can emerge. Only the dx^2-y^2 - and the s±-waves are robustly supported by the nearest-neighbor (NN) intra-orbital J 1 and the next-nearest-neighbor (NNN) intra-orbital J 2 antiferromagnetic (AFM) exchange couplings, respectively. This study suggests that the accurate initial input of the interaction parameters is essential to make FRG a useful method to determine the leading channel of superconducting instability.

  6. Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution

    PubMed Central

    Wagner, Dominic; Rinnenthal, Jörg; Narberhaus, Franz; Schwalbe, Harald

    2015-01-01

    The cyanobacterial hsp17 ribonucleicacid thermometer (RNAT) is one of the smallest naturally occurring RNAT. It forms a single hairpin with an internal 1×3-bulge separating the start codon in stem I from the ribosome binding site (RBS) in stem II. We investigated the temperature-dependent regulation of hsp17 by mapping individual base-pair stabilities from solvent exchange nuclear magnetic resonance (NMR) spectroscopy. The wild-type RNAT was found to be stabilized by two critical CG base pairs (C14-G27 and C13-G28). Replacing the internal 1×3 bulge by a stable CG base pair in hsp17rep significantly increased the global stability and unfolding cooperativity as evidenced by circular dichroism spectroscopy. From the NMR analysis, remote stabilization and non-nearest neighbour effects exist at the base-pair level, in particular for nucleotide G28 (five nucleotides apart from the side of mutation). Individual base-pair stabilities are coupled to the stability of the entire thermometer within both the natural and the stabilized RNATs by enthalpy–entropy compensation presumably mediated by the hydration shell. At the melting point the Gibbs energies of the individual nucleobases are equalized suggesting a consecutive zipper-type unfolding mechanism of the RBS leading to a dimmer-like function of hsp17 and switch-like regulation behaviour of hsp17rep. The data show how minor changes in the nucleotide sequence not only offset the melting temperature but also alter the mode of temperature sensing. The cyanobacterial thermosensor demonstrates the remarkable adjustment of natural RNATs to execute precise temperature control. PMID:25940621

  7. Cooper pairing in the insulating valence band in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Hu, Lun-Hui; Chen, Wei-Qiang; Zhang, Fu-Chun

    2015-04-01

    Conventional Cooper pairing arises from attractive interaction of electrons in the metallic bands. A recent experiment on Co-doped LiFeAs shows superconductivity in the insulating valence band, which is evolved from a metallic hole band upon doping. Here we examine this phenomenon by studying superconductivity in a three-orbital Hamiltonian relevant to the doped LiFeAs. We show explicitly that Cooper pairing of the insulating hole band requires a finite pairing interaction strength. For strong coupling, the superconductivity in the hole band is robust against the sink of the hole band below the Fermi level. Our theory predicts a substantial upward shift of the chemical potential in the superconducting transition for Co-doped LiFeAs.

  8. Statistics for critical clinical decision making based on readings of pairs of implanted sensors.

    PubMed

    Schmidtke, D W; Pishko, M V; Quinn, C P; Heller, A

    1996-09-01

    Low error rates are essential if lives of patients are to depend on readings of implanted sensors, such as glucose sensors in insulin-dependent diabetic patients. To verify the operation and to calibrate on demand an implanted sensor, it is necessary that calibration through a single, independent measurement involving withdrawal of only one sample of blood and its independent analysis be feasible. Such a one-point calibration must be accurate. Borrowing from nuclear reactor safety assurance, where a likelihood ratio test is applied to readings of pairs of pressure sensors for shutdown/no shutdown decisions, we apply a similar test to sensor pairs implanted in rats. We show, for five sets of glucose sensor pairs, calibrated in vivo by withdrawal of a single sample of blood, that application of the likelihood ratio test increases the fraction of the clinically correct readings from 92.4% for their averaged readings to 98.8%. PMID:8794921

  9. 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.

  10. Quantum heat engine based on photon-assisted Cooper pair tunneling

    NASA Astrophysics Data System (ADS)

    Hofer, Patrick P.; Souquet, J.-R.; Clerk, A. Â. A.

    2016-01-01

    We propose and analyze a simple mesoscopic quantum heat engine that exhibits both high power and high efficiency. The system consists of a biased Josephson junction coupled to two microwave cavities, with each cavity coupled to a thermal bath. Resonant Cooper pair tunneling occurs with the exchange of photons between cavities, and a temperature difference between the baths can naturally lead to a current against the voltage, and hence work. As a consequence of the unique properties of Cooper-pair tunneling, the heat current is completely separated from the charge current. This combined with the strong energy selectivity of the process leads to an extremely high efficiency.

  11. Identification and purification of a Drosophila protein that binds to the terminal 31-base-pair inverted repeats of the P transposable element

    SciTech Connect

    Rio, D.C.; Rubin, G.M.

    1988-12-01

    We have used DNase I footprinting and partially fractionated nuclear extracts from Drosophila Kc tissue culture cells to identify DNA-binding proteins that interact with the terminal repeats of P transposable elements. We have identified a binding activity that interacts specifically with a region of the 31-base-pair terminal inverted repeats that is directly adjacent to the duplication of target site DNA. Binding occurs to both the 5' and 3' inverted terminal repeats irrespective of the sequence of the duplicated target DNA. UV photochemical crosslinking studies suggest that the binding activity resides in a polypeptide of 65-70 kDa. Biochemical fractionation and oligonucleotide affinity chromatography have been used to purify the binding activity to near homogeneity and identify a polypeptide of 66 kDa in the highly purified preparations. The site to which binding occurs is included in a region absolutely required for P element transposition, suggesting that this binding protein may be a cellular factor involved in P element transposition.

  12. 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

  13. 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…

  14. 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…

  15. Exchange coupling between laterally adjacent nanomagnets.

    PubMed

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

    2016-09-30

    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. PMID:27535227

  16. 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

  17. 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

  18. Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

    PubMed Central

    Yang, Changwon; Kim, Eunae; Pak, Youngshang

    2015-01-01

    Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116

  19. Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base-Pair Oligodeoxynucleotide Duplex†

    PubMed Central

    Crenshaw, Charisse M.; Wade, Jacqueline E.; Arthanari, Haribabu; Frueh, Dominique; Lane, Benjamin F.; Núñez, Megan E.

    2011-01-01

    The base lesion 8-oxoguanine is formed readily by oxidation of DNA, potentially leading to G→T transversion mutations. Despite the apparent similarity of 8-oxoguanine-cytosine base pairs to normal guanine-cytosine base pairs, cellular base excision repair systems effectively recognize the lesion base. Here we apply several techniques to examine a single 8-oxoguanine lesion at the center of a nonpalindromic 15-mer duplex oligonucleotide in an effort to determine what, if anything, distinguishes an 8-oxoguanine-cytosine base pair from a normal base pair. The lesion duplex is globally almost indistinguishable from the unmodified parent duplex using CD spectroscopy and UV melting thermodynamics. The DNA mismatch-detecting photocleavage agent Rh(bpy)2chrysi3+ cleaves only weakly and nonspecifically, revealing that the 8oxoG-C pair is locally stable at the level of the individual base pairs. NMR spectra are also consistent with a well-conserved B-form duplex structure. In the 2D NOESY spectra, base-sugar and imino-imino crosspeaks are strikingly similar between parent and lesion duplexes. Changes in chemical shift due to the 8oxoG lesion are localized to its complementary cytosine and to the 2–3 base pairs immediately flanking the lesion on the lesion strand. Residues further removed from the lesion are shown to be unperturbed by its presence. Notably, imino exchange experiments indicate that the 8-oxoguanine-cytosine pair is strong and stable, with an apparent equilibrium constant for opening equal to that of other internal guanine-cytosine base pairs, on the order of 10−6. This collection of experiments shows that the 8-oxoguanine-cytosine base pair is incredibly stable and similar to the native pair. PMID:21902242

  20. 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

  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 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.

  3. Transition State in DNA Polymerase β Catalysis: Rate-Limiting Chemistry Altered by Base-Pair Configuration

    PubMed Central

    2015-01-01

    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

  4. Identifying alkali metal inhibitors of crystal growth: a selection criterion based on ion pair hydration energy.

    PubMed

    Farmanesh, Sahar; Alamani, Bryan G; Rimer, Jeffrey D

    2015-09-21

    We show that alkali metals function as effective modifiers of calcium oxalate monohydrate (COM) crystallization wherein alkali-oxalate ion parings reduce the rate of crystal growth by as much as 60%. Our findings reveal a distinct trend in alkali metal efficacy that cannot be explained by colloidal theories or simple descriptors, such as ion size, but is consistent with a theoretical model that accounts for the ion pair's affinity for water. PMID:26242310

  5. 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.

  6. UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke.

    PubMed

    Lee, Jae Young; Yang, Wei

    2006-12-29

    Helicases use the energy derived from nucleoside triphosphate hydrolysis to unwind double helices in essentially every metabolic pathway involving nucleic acids. Earlier crystal structures have suggested that DNA helicases translocate along a single-stranded DNA in an inchworm fashion. We report here a series of crystal structures of the UvrD helicase complexed with DNA and ATP hydrolysis intermediates. These structures reveal that ATP binding alone leads to unwinding of 1 base pair by directional rotation and translation of the DNA duplex, and ADP and Pi release leads to translocation of the developing single strand. Thus DNA unwinding is achieved by a two-part power stroke in a combined wrench-and-inchworm mechanism. The rotational angle and translational distance of DNA define the unwinding step to be 1 base pair per ATP hydrolyzed. Finally, a gateway for ssDNA translocation and an alternative strand-displacement mode may explain the varying step sizes reported previously. PMID:17190599

  7. 5S rRNA sequences from four marine invertebrates and implications for base pairing models of metazoan sequences.

    PubMed

    Walker, W F; Doolittle, W F

    1983-08-11

    The nucleotide sequences of 5S rRNAs from the starfish Asterias vulgaris, the squid Illex illecebrosus, the sipunculid Phascolopsis gouldii and the jellyfish Aurelia aurita were determined. The sequence from Asterias lends support for one of two previous base pairing models for helix E in metazoan sequences. The Aurelia sequence differs by five nucleotides from that previously reported and does not violate the consensus secondary structure model for eukaryotic 5S rRNA. PMID:6136024

  8. 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

  9. Oxygen Replacement with Selenium at the Thymidine 4-Position for the Se Base Pairing and Crystal Structure Studies

    SciTech Connect

    Salon,J.; Sheng, J.; Jiang, J.; Chen, G.; Caton-Williams, J.; Huang, Z.

    2007-01-01

    The T-A and C-G base pairing and stacking allow the formation of the stable DNA duplex structure for genetic information storage, transcription, and replication. To replace the oxygen of the nucleotide nucleobases with selenium for the studies of the base-pair recognition, the duplex stability, and the nuclei acid crystal structures, we have synthesized for the first time the 4-Se thymidine phosphoramidite and incorporated it into oligonucleotides via solid-phase synthesis with high coupling yield (99%). The Se modification on the nucleobase is relatively stable under the elevated temperature. Using the dU{sub Se} (2'-Se-dU) to facilitate the crystallization, we have successfully crystallized the DNA containing the 4-Se-T substitution and determined its structure at 1.50 {angstrom} resolution. The UV-melting and X-ray crystal structure studies have indicated that the Se substitution on the nucleobase does not cause a significant structure perturbation, the large Se atom on the thymine can be successfully accommodated by the DNA duplex, and the Se-mediated hydrogen bond (longer than the usual hydrogen bond) is formed within the modified T-A base pair. In addition, the Se derivatization on the nucleobases further facilitates X-ray crystal structure determination of nucleic acids and their protein complexes via Se MAD phasing.

  10. Higher-order structure of nucleic acids in the gas phase: top-down analysis of base-pairing interactions

    PubMed Central

    Fabris, D.; Kellersberger, K.A.; Wilhide, J.A.

    2012-01-01

    Non-ergodic as well as ergodic activation methods are capable of maintaining the integrity of base pairs during the top-down analysis of nucleic acids. Here, we investigate the significance of this characteristic in the investigation of higher-order structures of increasing complexity. We show that cognate fragments produced by typical backbone cleavages may not be always detected as separate sequence ions, but rather as individual products that remain associated through mutual pairing contacts. This effect translates into unintended masking of cleavage events that take place in double-stranded regions, thus leading to the preferential detection of fragments originating from unpaired regions. Such effect is determined by the stability of the weak non-covalent association between complementary stretches, which is affected by base composition, length of the double-stranded structure, and charge of the precursor ion selected for analysis. Although such effect may prevent the achievement of full sequence coverage for primary structure determination, it may provide the key to correctly differentiate double- versus single-stranded regions, in what could be defined as gas-phase footprinting experiments. In light of the critical role played by base pairs in defining the higher-order structure of nucleic acids, these approaches will be expected to support an increased utilization of mass spectrometry for the investigation of nucleic acid structure and dynamics. PMID:24027423

  11. Infrared spectrum of the Ag(+)-(pyridine)2 ionic complex: probing interactions in artificial metal-mediated base pairing.

    PubMed

    Chakraborty, Shamik; Dopfer, Otto

    2011-07-11

    The isolated pyridine-Ag(+)-pyridine unit (Py-Ag(+)-Py) is employed as a model system to characterize the recently observed Ag(+)-mediated base pairing in DNA oligonucleotides at the molecular level. The structure and infrared (IR) spectrum of the Ag(+)-Py(2) cationic complex are investigated in the gas phase by IR multiple-photon dissociation (IRMPD) spectroscopy and quantum chemical calculations to determine the preferred metal-ion binding site and other salient properties of the potential-energy surface. The IRMPD spectrum has been obtained in the 840-1720 cm(-1) fingerprint region by coupling the IR free electron laser at the Centre Laser Infrarouge d'Orsay (CLIO) with a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with an electrospray ionization source. The spectroscopic results are interpreted with quantum chemical calculations conducted at the B3LYP/aug-cc-pVDZ level. The analysis of the IRMPD spectrum is consistent with a σ complex, in which the Ag(+) ion binds to the nitrogen lone pairs of the two Py ligands in a linear configuration. The binding motif of Py-Ag(+)-Py in the gas phase is the same as that observed in Ag(+)-mediated base pairing in solution. Ag(+) bonding to the π-electron system of the aromatic ring is predicted to be a substantially less-favorable binding motif. PMID:21442717

  12. Estimation and optimization of loss-of-pair uncertainties based on PIV correlation functions

    NASA Astrophysics Data System (ADS)

    Scharnowski, Sven; Kähler, Christian J.

    2016-02-01

    The uncertainty quantification of particle image velocimetry (PIV) measurements is still an open problem, and to date, no consensus exists about the best suited approach. When the spatial resolution is not appropriate, the largest uncertainties are usually caused by flow gradients. But also the amount of loss-of-pairs due to out-of-plane flow motion and insufficient light-sheet overlap causes strong uncertainties in real experiments. In this paper, we show how the amount of loss-of-pairs can be quantified using the volume of the correlation function normalized by the volume of the autocorrelation function. The findings are an important step toward a reliable uncertainty estimation of instantaneous planar velocity fields computed from PIV and stereo-PIV data. Another important consequence of the analysis is that the results allow for the optimization of PIV and stereo-PIV setups in view of minimizing the total error. In particular, it is shown that the best results (concerning the relative uncertainty) can be achieved if the out-of-plane loss-of-correlation is smaller than one ( F o ). The only exception is the case where the out-of-plane motion is exactly zero. The predictions are confirmed experimentally in the last part of the paper.

  13. Reconstitution of biologically active 50S ribosomal subunits with artificial 5S RNA molecules carrying disturbances in the base pairing within the molecular stalk.

    PubMed Central

    Raué, H A; Lorenz, S; Erdmann, V A; Planta, R J

    1981-01-01

    Bacillus stearothermophilus 50S ribosomal subunits were reconstituted in vitro using artificial 5S RNA molecules constructed by combining parts of major and minor type (Raué et al. (1976) Europ. J. Biochem. 68, 169-176) B. licheniformis 5S RNA. The artificial 5S RNA molecules carry defined disturbances (A.C juxtapositions and extra G.U pairs) in the base pairing between the 5'- and 3'-terminal sequences of the molecule (the molecular stalk region). The biological activity of the reconstituted subunits was determined in an E. coli cell-free system programmed with poly-U. The results show that conservation of the base pairing within the molecular stalk is not required for biological activity of 5S RNA. Disturbances of the base pairing within this region do reduce the rate of reconstitution, however. Normal base pairing in the molecular stalk is thus required to ensure efficient ribosome assembly. PMID:6164987

  14. DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

    NASA Astrophysics Data System (ADS)

    Okutsu, N.; Shimamura, K.; Shimizu, E.; Shulga, S.; Danilov, V. I.; Kurita, N.

    2016-02-01

    To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH2 group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH2 group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (-0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.

  15. 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…

  16. Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs.

    PubMed Central

    Evertsz, E M; Rippe, K; Jovin, T M

    1994-01-01

    A 30 base pair parallel-stranded (ps) duplex ps-L1.L2 composed of two adjoined purine-purine and purine-pyrimidine sequence blocks has been characterized thermodynamically and spectroscopically. The 5'-terminal 15 residues in both strands ('left-half') consisted of the alternating d(GA)7G sequence that forms a ps homoduplex secondary structure stabilized by d(G.G) and d(A.A) base pairs. The 3'-terminal 15 positions of the sequence ('right-half') were combinations of A and T with complementary reverse Watson-Crick d(A.T) base pairing between the two strands. The characteristics of the full length duplex were compared to those of the constituent left and right halves in order to determine the compatibility of the two ps helical forms. The thermal denaturation curves and hyperchromicity profiles of all three duplexes determined by UV absorption spectroscopy were characteristic of ps-DNA, in accordance with previous studies. The thermodynamic properties of the 30 bp duplex corresponded within experimental error to the linear combination of the two 15-mers. Thus, the Tm and delta HvH of ps-L1.L2 in 10 mM MgCl2, derived from analyses according to a statistical mechanical formulation for the helix-coil transition, were 43 degrees C and 569 kJ mol-1, compared to 21 degrees C, 315 kJ mol-1 (ps-F5.F6) and 22 degrees C, 236 kJ mol-1 (ps-GA15). The UV absorption and CD spectra of ps-L1.L2 and the individual 15-mer ps motifs were also compared quantitatively. The sums of the two constituent native spectra (left+right halves) accurately matched that of the 30 bp duplex, with only small deviations in the 195-215 nm (CD) and 220-240 nm (absorption) regions. Based on analysis by native gel electrophoresis, the sequences studied formed duplex structures exclusively; there were no indications of higher order species. Chemical modification with diethyl pyrocarbonate showed no hyperreactivity of the junctional bases, indicating a smooth transition between the two parallel

  17. Interaction between adjacent lightning discharges in clouds

    NASA Astrophysics Data System (ADS)

    Wang, Yanhui; Zhang, Guangshu; Zhang, Tong; Li, Yajun; Wu, Bin; Zhang, Tinglong

    2013-07-01

    Using a 3D lightning radiation source locating system (LLS), three pairs of associated lightning discharges (two or more adjacent lightning discharges following an arbitrary rule that their space-gap was less than 10 km and their time-gap was less than 800 ms) were observed, and the interaction between associated lightning discharges was analyzed. All these three pairs of associated lightning discharges were found to involve three or more charge regions (the ground was considered as a special charge region). Moreover, at least one charge region involved two lightning discharges per pair of associated lightning discharges. Identified from electric field changes, the subsequent lightning discharges were suppressed by the prior lightning discharges. However, it is possible that the prior lightning discharge provided a remaining discharge channel to facilitate the subsequent lightning discharge. The third case provided evidence of this possibility. Together, the results suggested that, if the charges in the main negative charge region can be consumed using artificial lightning above the main negative charge regions, lightning accidents on the ground could be greatly reduced, on the condition that the height of the main negative charge region and the charge intensity of the lower positive charge region are suitable.

  18. 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.

  19. Photophysical and laser properties of cassettes based on a BODIPY and rhodamine pair.

    PubMed

    Gartzia-Rivero, Leire; Yu, Haibo; Bañuelos, Jorge; López-Arbeloa, Iñigo; Costela, Angel; Garcia-Moreno, Inmaculada; Xiao, Yi

    2013-12-01

    This work deals with the synthesis and the photophysical and laser properties of new BODIPY-rhodamine cassettes. These dyads differ in their rigid and conjugated spacer group (phenyl or acetylenephenyl) and in their linking positions (meta or para). The photophysical properties of these cassettes are controlled by the formation/opening of the spirolactone ring, which, in turn, switches off/on an energy-transfer process between the chromophores. Herein, we thoroughly describe the influence of the attached spacer group, as well as the distance and orientation between the donor-acceptor pair, on the excitation energy transfer. The observed fast dynamics and efficiency suggest that the process mainly takes place "through-bond", although the "through-space" mechanism also contributes to the whole process. As a result, efficient laser emission from the rhodamine is achieved upon excitation of the BODIPY, in particular for the cassette that contains an acetylenephenyl spacer group in a para disposition. PMID:24023008

  20. 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

  1. Headwater thermal response to partial-retention forest harvesting: a process-based paired-catchment experiment

    NASA Astrophysics Data System (ADS)

    Moore, R. D.; Guenther, S. M.; Gomi, T.

    2008-12-01

    Paired-catchment experiments are the most rigorous empirical research design for estimating the effects of land use on aquatic systems. However, they have recently come under increasing criticism, in part because past studies typically treated catchments as black boxes. As a result, investigators could only speculate about the factors responsible for any observed effects, limiting their ability to generalize the experimental results in space and time. This study used a paired-catchment approach to investigate the effects of partial- retention forest harvesting with no riparian buffer on the thermal regime of a headwater stream in coastal British Columbia. In addition to monitoring stream temperature at three locations within the treatment reach, we monitored above-stream microclimate, water surface evaporation, bed temperature profiles, groundwater temperature, and reach-scale surface-subsurface interaction. Daily maximum stream temperatures increased after harvesting by over 5 °C during summer, with little effect in winter. The major driver of post- harvest warming was an increase in solar radiation, which was partially moderated by the increased effects of hyporheic exchange, bed heat conduction and evaporation. Incorporating process-based measurements into paired-catchment experiments not only allows the causes of treatment response to be assessed, but they provide a valuable data set for testing predictive models.

  2. 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. PMID:24460544

  3. 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

  4. 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

  5. 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.

  6. Meiotic cohesin-based chromosome structure is essential for homologous chromosome pairing in Schizosaccharomyces pombe.

    PubMed

    Ding, Da-Qiao; Matsuda, Atsushi; Okamasa, Kasumi; Nagahama, Yuki; Haraguchi, Tokuko; Hiraoka, Yasushi

    2016-06-01

    Chromosome structure is dramatically altered upon entering meiosis to establish chromosomal architectures necessary for the successful progression of meiosis-specific events. An early meiotic event involves the replacement of the non-SMC mitotic cohesins with their meiotic equivalents in most part of the chromosome, forming an axis on meiotic chromosomes. We previously demonstrated that the meiotic cohesin complex is required for chromosome compaction during meiotic prophase in the fission yeast Schizosaccharomyces pombe. These studies revealed that chromosomes are elongated in the absence of the meiotic cohesin subunit Rec8 and shortened in the absence of the cohesin-associated protein Pds5. In this study, using super-resolution structured illumination microscopy, we found that Rec8 forms a linear axis on chromosomes, which is required for the organized axial structure of chromatin during meiotic prophase. In the absence of Pds5, the Rec8 axis is shortened whereas chromosomes are widened. In rec8 or pds5 mutants, the frequency of homologous chromosome pairing is reduced. Thus, Rec8 and Pds5 play an essential role in building a platform to support the chromosome architecture necessary for the spatial alignment of homologous chromosomes. PMID:26511279

  7. 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.

  8. 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. PMID:26698745

  9. G.T wobble base-pairing in Z-DNA at 1.0 A atomic resolution: the crystal structure of d(CGCGTG).

    PubMed Central

    Ho, P S; Frederick, C A; Quigley, G J; van der Marel, G A; van Boom, J H; Wang, A H; Rich, A

    1985-01-01

    The DNA oligomer d(CGCGTG) crystallizes as a Z-DNA double helix containing two guanine-thymine base pair mismatches of the wobble type. The crystal diffracts to 1 A resolution and the structure has been solved and refined. At this resolution, a large amount of information is revealed about the organization of the water molecules in the lattice generally and more specifically around the wobble base pairs. By comparing this structure with the analogous high resolution structure of d(CGCGCG) we can visualize the structural changes as well as the reorganization of the solvent molecules associated with wobble base pairing. There is only a small distortion of the Z-DNA backbone resulting from introduction of the GT mismatched base pairs. The water molecules cluster around the wobble base pair taking up all of the hydrogen bonding capabilities of the bases due to wobble pairing. These bridging water molecules serve to stabilize the base-base interaction and, thus, may be generally important for base mispairing either in DNA or in RNA molecules. PMID:4092690

  10. 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.

  11. 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. PMID:24788855

  12. Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs.

    PubMed

    Ohkubo, Akihiro; Yamada, Kenji; Ito, Yu; Yoshimura, Kiichi; Miyauchi, Koichiro; Kanamori, Takashi; Masaki, Yoshiaki; Seio, Kohji; Yuasa, Hideya; Sekine, Mitsuo

    2015-07-13

    A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2'-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (d(g)C) residue for a C-G base pair have higher binding and base recognition abilities than those containing 2'-OMe-4N-(2-guanidoethyl)-5-methylcytidine (2'-OMe (g)C), 2'-OMe-4N-(2-guanidoethyl)-5-methyl-2-thiocytidine (2'-OMe (g)Cs), d(g)C and 4S-(2-guanidoethyl)-4-thiothymidine ((gs)T). Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine ((DA)Nac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives. On the basis of this knowledge, we successfully synthesized a fully modified TFO containing (DA)Nac, d(g)C, 2'-OMe-2-thiothymidine (2'-OMe (s)T) and 2'-OMe-8-thioxoadenosine (2'-OMe (s)A) with high binding and base recognition abilities. To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions. PMID:26013815

  13. Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs

    PubMed Central

    Ohkubo, Akihiro; Yamada, Kenji; Ito, Yu; Yoshimura, Kiichi; Miyauchi, Koichiro; Kanamori, Takashi; Masaki, Yoshiaki; Seio, Kohji; Yuasa, Hideya; Sekine, Mitsuo

    2015-01-01

    A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2’-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (dgC) residue for a C-G base pair have higher binding and base recognition abilities than those containing 2’-OMe-4N-(2-guanidoethyl)-5-methylcytidine (2’-OMegC), 2’-OMe-4N-(2-guanidoethyl)-5-methyl-2-thiocytidine (2’-OMegCs), dgC and 4S-(2-guanidoethyl)-4-thiothymidine (gsT). Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine (DANac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives. On the basis of this knowledge, we successfully synthesized a fully modified TFO containing DANac, dgC, 2’-OMe-2-thiothymidine (2’-OMesT) and 2’-OMe-8-thioxoadenosine (2’-OMesA) with high binding and base recognition abilities. To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions. PMID:26013815

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

    PubMed

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

    2016-06-01

    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 (15)N-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

  15. 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.

  16. 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

  17. 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

  18. 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…

  19. 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

  20. Interaction of the main components from the traditional Chinese drug pair Chaihu-Shaoyao based on rat intestinal absorption.

    PubMed

    Chen, Yan; Wang, Jinyan; Yuan, Ling; Zhou, Lei; Jia, Xiaobin; Tan, Xiaobin

    2011-01-01

    The Chaihu-Shaoyao drug pair (Bupleuri Radix and Paeoniae Radix Alba) which is a traditional Chinese drug pair, has been widely used for anti-inflammatory purposes. Saikosaponin a (SSA), saikosaponin d (SSD) and paeoniflorin are identified as the main components in the pair. The present study focused on the interaction of the main components based on investigating their intestinal absorption using a four-site perfused rat intestinal model in order to clarify the mechanism of the compatibility of Chaihu-Shaoyao. The concentrations of SSA, SSD and paeoniflorin in the intestinal perfusate were determined by LC/MS or UPLC (Ultra Performance Liquid Chromatography) methods, followed by P*(eff) (effective permeability) and 10% ABS (the percent absorption of 10 cm of intestine) calculations. The results showed that all of the three main components displayed very low permeabilities (P*(eff) < 0.4), which implied their poor absorption in the rat intestine. The absorption levels of SSA and SSD were similar in intestine and higher in ileum than those in other intestinal regions in the decreasing order: colon, jejunum and duodenum. However, there is no significant difference in the absorption of paeoniflorin in the four segments (P < 0.05). The P*(eff) values of paeoniflorin exhibited an almost 2.11-fold or 1.90-fold increase in ileum when it was co-administrated with SSA and SSD, as well as 2.42-, 2.18-fold increase in colon, respectively, whereas the absorptions of SSA and SSD were not influenced by paeoniflorin. In conclusion, SSA and SSD could promote the absorption of paeoniflorin. To some extent this might explain the nature of the compatibility mechanisms of composite formulae in TCMs. PMID:22095024

  1. Winning Pairs.

    ERIC Educational Resources Information Center

    Monsour, Florence

    2000-01-01

    Mentoring programs that pair experienced and first-time teachers are gaining prominence in supporting, developing, and retaining new teachers. The successful Beginning Teacher Assistance program at University of Wisconsin-River Falls was designed to give new K-12 teachers the opportunity for yearlong, structured support from mentor teachers. (MLH)

  2. Post Hartree-Fock studies of the canonical Watson-Crick DNA base pairs: molecular structure and the nature of stability.

    PubMed

    Danilov, Victor I; Anisimov, Victor M

    2005-02-01

    Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6-31G(d) and 6-31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buckled geometry of G-C and A-T base pairs; while HF and DFT methods predict perfect planar or almost planar geometry of the base pairs. Supposedly the nonplanarity of the pairs is caused by pyramidalization of the amino nitrogen atoms, which is underestimated by the HF and DFT methods. This justifies the importance of geometry optimization at the MP2 level for obtaining reliable prediction of the charge distribution, molecular dipole moments and geometrical structure of the base pairs. The Morokuma-Kitaura and the Reduced Variational Space methods of the decomposition for molecular HF interaction energies were used for investigation of the hydrogen bonding in the Watson-Crick base pairs. It is shown that the HF stability of the hydrogen-bonded DNA base pairs originates mainly from electrostatic interactions. At the same time, the calculated magnitude of the second order intramolecular correlation correction to the Coulomb energy showed that electron correlation reduces the contribution of the electrostatic term to the attractive interaction for the A-T and G-C base pairs. Polarization, charge transfer and dispersion interactions also make considerable contribution to the attraction energy of bases. PMID:15588110

  3. 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

  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. 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

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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.

  8. 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

  9. 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

  10. 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. PMID:24921089

  11. 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 Central

    Sato, Takashi; Arai, Eri; Kohno, Takashi; Takahashi, Yoriko; Miyata, Sayaka; Tsuta, Koji; Watanabe, Shun-ichi; Soejima, Kenzo; Betsuyaku, Tomoko; Kanai, Yae

    2014-01-01

    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. PMID:24921089

  12. 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.

  13. Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems

    PubMed Central

    Ximenes, Camila; Brandão, Eduardo; Oliveira, Paula; Rocha, Abraham; Rego, Tamisa; Medeiros, Rafael; Aguiar-Santos, Ana; Ferraz, João; Reis, Christian; Araujo, Paulo; Carvalho, Luiz; Melo, Fabio L

    2014-01-01

    The Global Program for the Elimination of Lymphatic Filariasis (GPELF) aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR)-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuchereria bancrofti were collected during the day. Conventional PCR and semi-nested PCR assays were optimised. The detection limit of the technique for purified W. bancrofti DNA extracted from adult worms was 10 fg for the internal systems (WbF/Wb2) and 0.1 fg by using semi-nested PCR. The specificity of the primers was confirmed experimentally by amplification of 1 ng of purified genomic DNA from other species of parasites. Evaluation of the paired urine and serum samples by the semi-nested PCR technique indicated only two of the 20 tested individuals were positive, whereas the simple internal PCR system (WbF/Wb2), which has highly promising performance, revealed that all the patients were positive using both samples. This study successfully demonstrated the possibility of using the PCR technique on urine for the diagnosis of W. bancrofti infection. PMID:25424447

  14. Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA.

    PubMed

    Hithell, Gordon; Shaw, Daniel J; Donaldson, Paul M; Greetham, Gregory M; Towrie, Michael; Burley, Glenn A; Parker, Anthony W; Hunt, Neil T

    2016-05-01

    Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA. PMID:27079484

  15. Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.

    PubMed

    Alian, Akram; DeGiovanni, Andrew; Griner, Sarah L; Finer-Moore, Janet S; Stroud, Robert M

    2009-05-15

    Escherichia coli pseudouridine synthase RluF is dedicated to modifying U2604 in a stem-loop of 23S RNA, while a homologue, RluB, modifies the adjacent base, U2605. Both uridines are in the same RNA stem, separated by approximately 4 A. The 3.0 A X-ray crystal structure of RluF bound to the isolated stem-loop, in which U2604 is substituted by 5-fluorouridine to prevent catalytic turnover, shows RluF distinguishes closely spaced bases in similar environments by a selectivity mechanism based on a frameshift in base pairing. The RNA stem-loop is bound to a conserved binding groove in the catalytic domain. A base from a bulge in the stem, A2602, has folded into the stem, forcing one strand of the RNA stem to translate by one position and thus positioning U2604 to flip into the active site. RluF does not modify U2604 in mutant stem-loops that lack the A2602 bulge and shows dramatically higher activity for a stem-loop with a mutation designed to facilitate A2602 refolding into the stem with concomitant RNA strand translation. Residues whose side chains contact rearranged bases in the bound stem-loop, while conserved among RluFs, are not conserved between RluFs and RluBs, suggesting that RluB does not bind to the rearranged stem loop. PMID:19298824

  16. Crystal Structure of an RluF–RNA Complex: A Base-Pair Rearrangement Is the Key to Selectivity of RluF for U2604 of the Ribosome

    PubMed Central

    Alian, Akram; DeGiovanni, Andrew; Griner, Sarah L.; Finer-Moore, Janet S.; Stroud, Robert M.

    2009-01-01

    Escherichia coli pseudouridine synthase RluF is dedicated to modifying U2604 in a stem–loop of 23S RNA, while a homologue, RluB, modifies the adjacent base, U2605. Both uridines are in the same RNA stem, separated by ~4 Å. The 3.0 Å X-ray crystal structure of RluF bound to the isolated stem–loop, in which U2604 is substituted by 5-fluorouridine to prevent catalytic turnover, shows RluF distinguishes closely spaced bases in similar environments by a selectivity mechanism based on a frameshift in base pairing. The RNA stem–loop is bound to a conserved binding groove in the catalytic domain. A base from a bulge in the stem, A2602, has folded into the stem, forcing one strand of the RNA stem to translate by one position and thus positioning U2604 to flip into the active site. RluF does not modify U2604 in mutant stem–loops that lack the A2602 bulge and shows dramatically higher activity for a stem–loop with a mutation designed to facilitate A2602 refolding into the stem with concomitant RNA strand translation. Residues whose side chains contact rearranged bases in the bound stem–loop, while conserved among RluFs, are not conserved between RluFs and RluBs, suggesting that RluB does not bind to the rearranged stem loop. PMID:19298824

  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. PMID:24960611

  18. 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

  19. The USH1C 216G-->A splice-site mutation results in a 35-base-pair deletion.

    PubMed

    Lentz, Jennifer; Savas, Sevtap; Ng, San-San; Athas, Grace; Deininger, Prescott; Keats, Bronya

    2005-02-01

    Usher syndrome is characterized by profound hearing loss and retinal degeneration. A splice-site mutation, 216G-->A, in exon 3 of USH1C is associated with Acadian Usher type IC. This mutation was reported to create an in-frame deletion of 39 base pairs (bp), resulting in an unstable transcript. By RT-PCR analysis of 216A and 216G constructs transfected into HeLa cells and also of patient cell lines, we have demonstrated a frame-shift deletion of 35 bp, not 39 bp. Thus, the instability of the USH1C mRNA is explained by the 216G-->A out-of-frame splice site mutation. PMID:15578223

  20. End-to-end stacking and liquid crystal condensation of 6- to 20-base pair DNA duplexes.

    SciTech Connect

    Nakata, M.; Zanchetta, G.; Chapman, B.D.; Christopher, D.; Jones, D.; Cross, J.O.; Pindak, R.; Bellini, T.; Noel, N.; X-Ray Science Division; Univ. of Colorado; Univ. di Milano; BNL

    2007-11-23

    Short complementary B-form DNA oligomers, 6 to 20 base pairs in length, are found to exhibit nematic and columnar liquid crystal phases, even though such duplexes lack the shape anisotropy required for liquid crystal ordering. Structural study shows that these phases are produced by the end-to-end adhesion and consequent stacking of the duplex oligomers into polydisperse anisotropic rod-shaped aggregates, which can order into liquid crystals. Upon cooling mixed solutions of short DNA oligomers, in which only a small fraction of the DNA present is complementary, the duplex-forming oligomers phase-separate into liquid crystal droplets, leaving the unpaired single strands in isotropic solution. In a chemical environment where oligomer ligation is possible, such ordering and condensation would provide an autocatalytic link whereby complementarity promotes the extended polymerization of complementary oligomers.

  1. Theoretical study of the protonation of the one-electron-reduced guanine-cytosine base pair by water.

    PubMed

    Hsu, Sodio C N; Wang, Tzu-Pin; Kao, Chai-Lin; Chen, Hui-Fen; Yang, Po-Yu; Chen, Hsing-Yin

    2013-02-21

    Prototropic equilibria in ionized DNA play an important role in charge transport and radiation damage of DNA and, therefore, continue to attract considerable attention. Although it is well-established that electron attachment will induce an interbase proton transfer from N1 of guanine (G) to N3 of cytosine (C), the question of whether the surrounding water in the major and minor grooves can protonate the one-electron-reduced G:C base pair still remains open. In this work, density functional theory (DFT) calculations were employed to investigate the energetics and mechanism for the protonation of the one-electron-reduced G:C base pair by water. Through the calculations of thermochemical cycles, the protonation free energies were estimated to be in the range of 11.6-14.2 kcal/mol. The calculations for the models of C(•-)(H(2)O)(8) and G(-H1)(-)(H(2)O)(16), which were used to simulate the detailed processes of protonation by water before and after the interbase proton transfer, respectively, revealed that the protonation proceeds through a concerted double proton transfer involving the water molecules in the first and second hydration shells. Comparing the present results with the rates of interbase proton transfer and charge transfer along DNA suggests that protonation on the C(•-) moiety is not competitive with interbase proton transfer, but the possibility of protonation on the G(-H1)(-) moiety after interbase proton transfer cannot be excluded. Electronic-excited-state calculations were also carried out by the time-dependent DFT approach. This information is valuable for experimental identification in the future. PMID:23363248

  2. Dynamics and couplings of N-H stretching excitations of guanosine-cytidine base pairs in solution.

    PubMed

    Yang, Ming; Szyc, Łukasz; Röttger, Katharina; Fidder, Henk; Nibbering, Erik T J; Elsaesser, Thomas; Temps, Friedrich

    2011-05-12

    N-H stretching vibrations of hydrogen-bonded guanosine-cytidine (G·C) base pairs in chloroform solution are studied with linear and ultrafast nonlinear infrared (IR) spectroscopy. Assignment of the IR-active bands in the linear spectrum is made possible by combining structural information on the hydrogen bonds in G·C base pairs with literature results of density functional theory calculations, and empirical relations connecting frequency shifts and intensity of the IR-active vibrations. A local mode representation of N-H stretching vibrations is adopted, consisting of ν(G)(NH(2))(f) and ν(C)(NH(2))(f) modes for free NH groups of G and C, and of ν(G)(NH(2))(b), ν(G)(NH), and ν(C)(NH(2))(b) modes associated with N-H stretching motions of hydrogen-bonded NH groups. The couplings and relaxation dynamics of the N-H stretching excitations are studied with femtosecond mid-infrared two-dimensional (2D) and pump-probe spectroscopy. The N-H stretching vibrations of the free NH groups of G and C have an average population lifetime of 2.4 ps. Besides a vibrational population lifetime shortening to subpicosecond values observed for the hydrogen-bonded N-H stretching vibrations, the 2D spectra reveal vibrational excitation transfer from the ν(G)(NH(2))(b) mode to the ν(G)(NH) and/or ν(C)(NH(2))(b) modes. The underlying intermode vibrational couplings are on the order of 10 cm(-1). PMID:21244064

  3. 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.

  4. 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

  5. Electron pairing without superconductivity

    NASA Astrophysics Data System (ADS)

    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

    2015-05-01

    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.

  6. 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.

  7. Magnon-mediated pairing and isotope effect in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Wu, Jiansheng; Phillips, Philip

    2011-03-01

    Within a minimal model for the iron-based superconductors in which itinerant electrons interact with a band of local moments, we derive a general conclusion for multiband superconductivity. In a multiband superconductor, due to the Adler theorem, the interband scattering dominates the intraband scattering at the long wavelength limit as long as both interactions are induced by the Goldstone boson (which is the magnon in our case) and the transferred momentum is non-zero. Such an interaction leads to a well known sign-reversing superconductivity even if the interband and intraband interaction are repulsive. This effect can be modeled as arising from an internal Josephson link between the Fermi surface sheets. Our model is also consistent with the recently discovered coexistence of superconductivity and magnetic order in iron-pnictides. Although the experimentally observed isotope effect is large, α = 0.4, we show that it is consistent with a non-phononic mechanism in which it is the isotope effects which result in a change in the lattice constant and, as a consequence, the zero-point motion of the Fe atoms.

  8. Effect of pairing fluctuations on the spin resonance in Fe-based superconductors

    NASA Astrophysics Data System (ADS)

    Hinojosa, Alberto; Chubukov, Andrey V.; Wölfle, Peter

    2014-09-01

    The spin resonance observed in the inelastic neutron scattering data on Fe-based superconductors has played a prominent role in the quest for determining the symmetry of the order parameter in these compounds. Most theoretical studies of the resonance employ an RPA-type approach in the particle-hole channel and associate the resonance in the spin susceptibility χS(q,ω) at momentum Q =(π,π) with the spin-exciton of an s+- superconductor, pulled below 2Δ by residual attraction associated with the sign change of the gap between Fermi points connected by Q. Here we explore the effect of fluctuations in the particle-particle channel on the spin resonance. Particle-particle and particle-hole channels are coupled in a superconductor and to what extent the spin resonance can be viewed as a particle-hole exciton needs to be addressed. In the case of purely repulsive interactions, we find that the particle-particle channel at total momentum Q (the π channel) contributes little to the resonance. However, if the interband density-density interaction is attractive and the π resonance is possible on its own, along with spin-exciton, we find a much stronger shift of the resonance frequency from the position of the would-be spin-exciton resonance. We also show that the expected double-peak structure in this situation does not appear because of the strong coupling between particle-hole and particle-particle channels, and ImχS(Q ,ω) displays only a single peak.

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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/. PMID:26080082

  16. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs

    PubMed Central

    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 in10-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/. PMID:26080082

  17. Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis.

    PubMed

    Hikida, Yasushi; Kimoto, Michiko; Yokoyama, Shigeyuki; Hirao, Ichiro

    2010-07-01

    Methods for fluorescent probing at a defined position of RNA provide powerful tools for analyzing the local structural conformation of functional RNA molecules by tracking fluorescence changes. In this article, we describe the site-specific fluorescent probing of RNA by transcription with an expanded genetic alphabet, using an extra, unnatural base pair between 2-amino-6-(2-thienyl)purine (s) and pyrrole-2-carbaldehyde (Pa). The protocol comprises template DNA preparation containing Pa, transcription involving fluorescent s incorporation and structural analysis of transcripts. The s base is strongly fluorescent, and its nucleoside 5'-triphosphate is site-specifically incorporated into RNA transcripts, opposite Pa in DNA templates, by conventional T7 transcription. The fluorescent intensity of s changes depending on its environment around the probe site, providing clues about the local structural features of RNA molecules. This is the first protocol for RNA transcript preparation with fluorescent labeling at a desired position. The procedure for s-containing RNA preparation takes about 2-3 d. PMID:20595959

  18. 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.

  19. 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.

  20. 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. PMID:23531077

  1. Testing the dx2-y2*-wave pairing symmetry by quasiparticle interference and Knight shift in BiS2-based superconductors

    NASA Astrophysics Data System (ADS)

    Gao, Yi; Zhou, Tao; Huang, Huaixiang; Tong, Peiqing; Wang, Qiang-Hua

    2014-08-01

    The quasiparticle interference (QPI) patterns in BiS2-based superconductors are theoretically investigated by taking into account the spin-orbital coupling and assuming the recently proposed dx2-y2*-wave pairing symmetry. We found two distinct scattering wave vectors whose evolution can be explained based on the evolution of the constant-energy contours. In addition, we also studied the QPI spectra in the conventional s-wave, d-wave, and extended s-wave cases and propose to further measure the Knight shift to distinguish the dx2-y2*-wave pairing from the d-wave one. The QPI spectra as well as the Knight shift presented in this paper can thus be compared with future scanning tunneling microscopy and NMR experiments to test whether the pairing symmetry is dx2-y2* wave in BiS2-based superconductors.

  2. Ambiguities in the elastic scattering of 8 MeV neutrons from adjacent nuclei

    NASA Astrophysics Data System (ADS)

    Lawson, R. D.; Guenther, P. T.; Smith, A. B.

    1990-12-01

    Ratios of the cross sections for the elastic scattering of 8 MeV neutrons from adjacent nuclei are measured over the angular range ~ 20°-160° for the target pairs 51V/Cr, 59Co/ 58Ni, Cu/Zn, 89Y/ 93Nb, 89Y/Zr, 93Nb/Zr, In/Cd and 209Bi/Pb. The observed ratios vary from unity by as much as a factor of ~2 at some angles for the lighter target pairs. The ratios are generally consistent with a model based upon a real Woods-Saxon potential whose geometry is essentially constant between pairs, and whose strength has an ( N- Z)/ A (symmetry) component with a magnitude of ~ 16 MeV. For pairs with A > 100, a constant-geometry derivative Woods-Saxon imaginary potential, with a symmetry strength of ~15 MeV, explains the ratios. However, for the lighter nuclei, the difffuseness of the imaginary potential varies rapidly near the N = 28 and N = 50 shell closures, and for the 59Co- 58Ni and Cu-Zn pairs, the imaginary symmetry-potential strength is about twice the 15 MeV global value. A method for approximating the spin-spin potential is given, and it is shown that this interaction makes a negligible contribution to the calculated ratios. However, channel coupling can lead to large reorientation effects which can substantially change the calculated ratios. Differences in the spin-orbit interaction between neighboring pairs can significantly affect the calculated ratios.

  3. Full analysis of multi-photon pair effects in spontaneous parametric down conversion based photonic quantum information processing

    NASA Astrophysics Data System (ADS)

    Takeoka, Masahiro; Jin, Rui-Bo; Sasaki, Masahide

    2015-04-01

    In spontaneous parametric down conversion (SPDC) based quantum information processing (QIP) experiments, there is a tradeoff between the coincidence count rates (i.e. the pumping power of the SPDC), which limits the rate of the protocol, and the visibility of the quantum interference, which limits the quality of the protocol. This tradeoff is mainly caused by the multi-photon pair emissions from the SPDCs. In theory, the problem is how to model the experiments without truncating these multi-photon emissions while including practical imperfections. In this paper, we establish a method to theoretically simulate SPDC-based QIPs which fully incorporates the effect of multi-photon emissions and various practical imperfections. The key ingredient in our method is the application of the characteristic function formalism which has been used in continuous variable QIPs. We apply our method to three examples, the Hong-Ou-Mandel interference and the Einstein-Podolsky-Rosen interference experiments, and the concatenated entanglement swapping protocol. For the first two examples, we show that our theoretical results quantitatively agree with the recent experimental results. Also we provide the closed expressions for these interference visibilities with the full multi-photon components and various imperfections. For the last example, we provide the general theoretical form of the concatenated entanglement swapping protocol in our method and show the numerical results up to five concatenations. Our method requires only a small computational resource (a few minutes by a commercially available computer), which was not possible in the previous theoretical approach. Our method will have applications in a wide range of SPDC-based QIP protocols with high accuracy and a reasonable computational resource.

  4. 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. PMID

  5. 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

  6. 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

  7. RNA structure analysis using methidiumpropyl-EDTA.Fe(II): a base-pair-specific RNA structure probe.

    PubMed Central

    Vary, C P; Vournakis, J N

    1984-01-01

    Methidiumpropyl-EDTA.Fe(II) [MPE.Fe(II)] in the presence of dithiothreitol, is shown to cleave phenylalanine-accepting tRNA (tRNAPhe) in a structure-specific fashion. Molar ratios of MPE.Fe(II) to tRNAPhe of less than 1 preferentially cleave phosphodiester bonds known to occur in double-stranded regions of the tRNAPhe molecule. Microdensitometric analysis of autoradiograms of MPE.Fe(II) cleavage products following gel electrophoresis reveals a correspondence between preferred sites of MPE.Fe(II) cleavage and sites in tRNAPhe most sensitive to cobra venom ribonuclease, a double-strand-specific endoribonuclease. Conversely, sites of cleavage by the single-strand-specific S1 nuclease correspond to those nucleotides that are least susceptible to MPE.Fe(II) hydrolysis. Sensitive helical regions in tRNAPhe include the dihydrouracil and the "T psi C" stems, which cannot be detected by cobra venom ribonuclease because of steric constraints. Phosphodiester bonds within the T psi C and dihydrouracil loop regions, which are not detected by S1 nuclease under rigorously controlled digestion conditions, are revealed by inference from their relative insensitivity to MPE.Fe(II). These results demonstrate the utility of MPE.Fe(II) as a general small molecular weight probe of RNA structure, having a greater accessibility to base-paired regions than do the more bulky enzymic probes. Images PMID:6209709

  8. 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. PMID:26279621

  9. Spectrophotometric Determination of Cefixime Trihydrate in Pharmaceutical Formulations Based on Ion-Pair Reaction with Bromophenol Blue

    PubMed Central

    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. PMID:26279621

  10. 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.

  11. 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. PMID:26621073

  12. Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution

    PubMed Central

    Hwang, Candy S.; Xu, Liang; Wang, Wei; Ulrich, Sébastien; Zhang, Lu; Chong, Jenny; Shin, Ji Hyun; Huang, Xuhui; Kool, Eric T.; McKenna, Charles E.; Wang, Dong

    2016-01-01

    RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous ‘synthetic nucleic acid substitution’ strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β,γ-bridging atom-‘substituted’ NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β,γ-methylene substitution on the non-cognate UTP/dT scaffold (∼3-fold decrease in kpol) is significantly different from that of the cognate ATP/dT scaffold (∼130-fold decrease in kpol). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation. PMID:27060150

  13. Can tautomerization of the A·T Watson-Crick base pair via double proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis.

    PubMed

    Brovarets, Ol'ha O; Hovorun, Dmytro M

    2014-01-01

    Trying to answer the question posed in the title, we have carried out a detailed theoretical investigation of the biologically important mechanism of the tautomerization of the A·T Watson-Crick DNA base pair, information that is hard to establish experimentally. By combining theoretical investigations at the MP2 and density functional theory levels of QM theory with quantum theory of atoms in molecules analysis, the tautomerization of the A·T Watson-Crick base pair by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ϵ = 4) corresponding to a hydrophobic interfaces of protein-nucleic acid interactions. Based on the sweeps of the electron-topological, geometric, and energetic parameters, which describe the course of the tautomerization along its intrinsic reaction coordinate (IRC), it was proved that the A·T → A(∗)·T(∗) tautomerization through the DPT is a concerted (i.e. the pathway without an intermediate) and asynchronous (i.e. protons move with a time gap) process. The limiting stage of this phenomenon is the final PT along the N6H⋯O4 hydrogen bond (H-bond). The continuum with ϵ = 4 does not affect qualitatively the course of the tautomerization reaction: similar to that observed in vacuo, it proceeds via a concerted asynchronous process with the same structure of the transition state (TS). For the first time, the nine key points along the IRC of the A·T base pair tautomerization, which could be considered as electron-topological "fingerprints" of a concerted asynchronous process of the tautomerization via the DPT, have been identified and fully characterized. These nine key points have been used to define the reactant, TS, and product regions of the DPT in the A·T base pair. Considering the energy dependence of each of the three H-bonds, which stabilize the Watson-Crick and Löwdin's base pairs, along the IRC of the tautomerization, it was found that all these H

  14. Unravelling the interaction dynamics of a carbonatite-silicate magmatic pair: A numerical approach based on Korteweg Stress theory

    NASA Astrophysics Data System (ADS)

    Valentini, L.; Moore, K. R.; Chazot, G.

    2009-04-01

    Most of the worldwide carbonatites occur in spatial association with silicate rocks. Even when unquestionable evidence for the associated carbonatite and silicate rocks to represent contemporaneous liquids exists, the modes of interaction between the two liquids can be difficult to infer. In general, the retrieval of information about the mechanisms of interaction between magmas can be complicated by the intrinsic dynamical nature of such systems. The development of new physico-chemical equilibria (e.g. hybridization) can erase any information about the previous stages of interaction. However, the occurrence of magmatic heterogeneities, such as enclaves and flow bands, as well as mineral disequilibrium textures, may serve as dynamic markers for the underlying interaction processes. Small-scale heterogeneities, in the form of micron to millimetre sized globules, characterized by more or less smooth interfaces, are frequently observed in carbonatite-silicate pairs. Textural observation, as well as the lack of suitable mechanisms for the dispersion of a discrete magmatic liquid in the form of a small-scale emulsion, have lead many petrologists to advocate immiscible separation as the process capable of forming such textures. However, the geochemical criteria for liquid immiscibility are not always met, and when not coupled with geochemical and dynamical arguments, textural observation may lead to ambiguous conclusions. In this study we adopted an integrated approach in order to infer the details of magmatic interaction of a carbonatite-silicate pair from Massif Central (France). The studied samples display emulsion-like textures, formed by micro-scale dolomitic globules dispersed in a trachytic glassy matrix. Our approach is based on a novel numerical method, coupled with textural observation and geochemical analyses. The novelty of our numerical model consists in the inclusion, in the adopted advection-diffusion equations, of a term that takes into account the effect

  15. 46 CFR 148.445 - Adjacent spaces.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 5 2013-10-01 2013-10-01 false Adjacent spaces. 148.445 Section 148.445 Shipping COAST... THAT REQUIRE SPECIAL HANDLING Additional Special Requirements § 148.445 Adjacent spaces. When... 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, 2014 CFR

    2014-10-01

    ... 46 Shipping 5 2014-10-01 2014-10-01 false Adjacent spaces. 148.445 Section 148.445 Shipping COAST... THAT REQUIRE SPECIAL HANDLING Additional Special Requirements § 148.445 Adjacent spaces. When... 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, 2012 CFR

    2012-10-01

    ... 46 Shipping 5 2012-10-01 2012-10-01 false Adjacent spaces. 148.445 Section 148.445 Shipping COAST... THAT REQUIRE SPECIAL HANDLING Additional Special Requirements § 148.445 Adjacent spaces. When... 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, 2011 CFR

    2011-10-01

    ... 46 Shipping 5 2011-10-01 2011-10-01 false Adjacent spaces. 148.445 Section 148.445 Shipping COAST... THAT REQUIRE SPECIAL HANDLING Additional Special Requirements § 148.445 Adjacent spaces. When... following requirements must be met: (a) Each space adjacent to a cargo hold must be ventilated by...

  19. 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.

  20. 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

  1. 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

  2. Electron Pairing Without Superconductivity

    NASA Astrophysics Data System (ADS)

    Levy, Jeremy; Cheng, G.; Tomczyk, M.; Lu, S.; Veazey, J. P.; Huang, M.; Irvin, P.; Ryu, S.; Lee, H.; Eom, C.-B.; Hellberg, C. S.

    2015-03-01

    Strontium titanate (SrTiO3) exhibits an extremely low carrier density threshold for superconductivity, and possesses a phase diagram similar to high-temperature superconductors--two factors that suggest an unconventional pairing mechanism. We describe transport experiments with nanowire-based quantum dots localized at the interface between SrTiO3 and LaAlO3. Electrostatic gating of the quantum dot reveals a series of two-electron conductance resonances--paired electron states--that bifurcate above a critical magnetic field Bp 1-4 Tesla, an order of magnitude larger than the superconducting critical magnetic field. For B Bp, the resonances exhibit a linear Zeeman-like energy splitting. Electron pairing is stable at temperatures as high as T = 900 mK, far above the superconducting transition temperature (Tc 300 mK). 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 an attractive-U Hubbard model that describes real-space electron pairing as a precursor to superconductivity. This work was supported by ARO MURI W911NF-08-1-0317 (J.L.), AFOSR MURI FA9550-10-1-0524 (C.-B.E., J.L.) and FA9550-12-1-0342 (C.-B.E.), and grants from the National Science Foundation DMR-1104191 (J.L.), DMR.

  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. Design and Synthesis of Heterocyclic Cations for Specific DNA Recognition: From AT-Rich to Mixed-Base-Pair DNA Sequences

    PubMed Central

    2015-01-01

    The compounds synthesized in this research were designed with the goal of establishing a new paradigm for mixed-base-pair DNA sequence-specific recognition. The design scheme starts with a cell-permeable heterocyclic cation that binds to AT base pair sites in the DNA minor groove. Modifications were introduced in the original compound to include an H-bond accepting group to specifically recognize the G-NH that projects into the minor groove. Therefore, a series of heterocyclic cations substituted with an azabenzimidazole ring has been designed and synthesized for mixed-base-pair DNA recognition. The most successful compound, 12a, had an azabenzimidazole to recognize G and additional modifications for general minor groove interactions. It binds to the DNA site −AAAGTTT– more strongly than the −AAATTT– site without GC and indicates the design success. Structural modifications of 12a generally weakened binding. The interactions of the new compound with a variety of DNA sequences with and without GC base pairs were evaluated by thermal melting analysis, circular dichroism, fluorescence emission spectroscopy, surface plasmon resonance, and molecular modeling. PMID:24422528

  5. The crystal structure of N4-methylcytosine.guanosine base-pairs in the synthetic hexanucleotide d(CGCGm4CG).

    PubMed Central

    Cervi, A R; Guy, A; Leonard, G A; Téoule, R; Hunter, W N

    1993-01-01

    The structure of d(CGCGm4CG) were m4C = N4-methylcytosine has been determined by crystallographic methods. The crystals are multifaced prisms, with orthorhombic space group P2(1)2(1)2(1) and unit cell dimensions of a = 17.98, b = 30.77 and c = 44.75A. The asymmetric unit consists of one duplex of hexanucleotide and 49 waters. The R-factor is 0.189 for 1495 reflections with F > or = sigma(F) to a resolution limit of 1.8A. The double helix has a Z-DNA type structure which appears to be intermediate in structure to the two previously characterised structure types for Z-DNA hexamers. The two m4C.G base-pairs adopt structures that are very similar to those of the equivalent base-pairs in the structure of the native sequence d(CGCGCG) except for the presence of the methyl groups which are trans to the N3 atoms of their parent nucleotides and protrude into the solvent region. The introduction of the modified base-pairs into the d(CGCGCG) duplex appears to have a minimal effect on the overall base-pair morphology of the Z-DNA duplex. Images PMID:8284207

  6. ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets

    PubMed Central

    2014-01-01

    Background We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end sequencing can achieve complete overlap of read pairs. Variant calling from Hi-Plex-derived datasets can thus rely on the identification of variants appearing in both reads of read-pairs, permitting stringent filtering of sequencing chemistry-induced errors. These principles underly ROVER software (derived from Read Overlap PCR-MPS variant caller), which we have recently used to report the screening for genetic mutations in the breast cancer predisposition gene PALB2. Here, we describe the algorithms underlying ROVER and its usage. Results ROVER enables users to quickly and accurately identify genetic variants from PCR-targeted, overlapping paired-end MPS datasets. The open-source availability of the software and threshold tailorability enables broad access for a range of PCR-MPS users. Methods ROVER is implemented in Python and runs on all popular POSIX-like operating systems (Linux, OS X). The software accepts a tab-delimited text file listing the coordinates of the target-specific primers used for targeted enrichment based on a specified genome-build. It also accepts aligned sequence files resulting from mapping to the same genome-build. ROVER identifies the amplicon a given read-pair represents and removes the primer sequences by using the mapping co-ordinates and primer co-ordinates. It considers overlapping read-pairs with respect to primer-intervening sequence. Only when a variant is observed in both reads of a read-pair does the signal contribute to a tally of read-pairs containing or not containing the variant. A user-defined threshold informs the minimum number of, and proportion of, read-pairs a variant must be observed in for a ‘call’ to be made. ROVER also reports the depth of coverage across amplicons to facilitate the

  7. Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific.

    PubMed

    Redd, A J; Takezaki, N; Sherry, S T; McGarvey, S T; Sofro, A S; Stoneking, M

    1995-07-01

    Length changes in human mitochondrial DNA (mtDNA) are potentially useful markers for inferring the evolutionary history of populations. One such length change is a nine base pair (9-bp) deletion that is located in the intergenic region between the COII gene and the Lysine tRNA gene (COII/tRNALys intergenic region). This deletion has been used as a genetic marker to trace descent from peoples of East Asian origin. A geographic cline of the deletion frequency across modern Pacific Islander populations suggests that the deletion may be useful for tracing prehistoric Polynesian origins and affinities. Mitochondrial DNA sequence variation within two variable segments of the control region (CR) permits a number of inferences regarding the evolutionary history of the 9-bp deletion that cannot be determined from frequency data alone. We obtained CR sequences from 74 mtDNAs with the 9-bp deletion from Indonesia, coastal Papua New Guinea (PNG), and American Samoa. Phylogenetic and pairwise distribution analysis of these CR sequences pooled with previously published CR sequences reveals that the deletion arose independently in Africa and Asia and suggests possible multiple origins of the deletion in Asia. A clinal increase of the frequency of the 9-bp deletion across the three Pacific populations is associated with a decrease in CR sequence diversity, consistent with founder events. Furthermore, analysis of pairwise difference distributions indicates an expansion time of proto-Polynesians that began 5,500 yr ago from Southeast Asia. These results are consistent with the express train model of Polynesian origins. PMID:7659016

  8. N-H stretching vibrations of guanosine-cytidine base pairs in solution: ultrafast dynamics, couplings, and line shapes.

    PubMed

    Fidder, Henk; Yang, Ming; Nibbering, Erik T J; Elsaesser, Thomas; Röttger, Katharina; Temps, Friedrich

    2013-02-01

    Dynamics and couplings of N-H stretching vibrations of chemically modified guanosine-cytidine (G·C) base pairs in chloroform are investigated with linear infrared spectroscopy and ultrafast two-dimensional infrared (2D-IR) spectroscopy. Comparison of G·C absorption spectra before and after H/D exchange reveals significant N-H stretching absorption in the region from 2500 up to 3300 cm(-1). Both of the local stretching modes ν(C)(NH(2))(b) of the hydrogen-bonded N-H moiety of the cytidine NH(2) group and ν(G)(NH) of the guanosine N-H group contribute to this broad absorption band. Its complex line shape is attributed to Fermi resonances of the N-H stretching modes with combination and overtones of fingerprint vibrations and anharmonic couplings to low-frequency modes. Cross-peaks in the nonlinear 2D spectra between the 3491 cm(-1) free N-H oscillator band and the bands centered at 3145 and 3303 cm(-1) imply N-H···O═C hydrogen bond character for both of these transitions. Time evolution illustrates that the 3303 cm(-1) band is composed of a nearly homogeneous band absorbing at 3301 cm(-1), ascribed to ν(G)(NH(2))(b), and a broad inhomogeneous band peaking at 3380 cm(-1) with mainly guanosine carbonyl overtone character. Kinetics and signal strengths indicate a <0.2 ps virtually complete population transfer from the excited ν(G)(NH(2))(b) mode to the ν(G)(NH) mode at 3145 cm(-1), suggesting lifetime broadening as the dominant source for the homogeneous line shape of the 3301 cm(-1) transition. For the 3145 cm(-1) band, a 0.3 ps population lifetime was obtained. PMID:23317104

  9. 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. PMID:24816369

  10. Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2′-deoxyadenosine:dT Base Pairing in DNA

    PubMed Central

    2011-01-01

    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 Å resolution in the presence of Mg2+. 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. PMID:22059929

  11. 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.

  12. 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.

  13. 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

  14. Synthesis of 5-[3-(2-aminopyrimidin-4-yl)aminopropyn-1-yl]uracil derivative that recognizes Ade-Thy base pairs in double-stranded DNA.

    PubMed

    Ito, Yu; Masaki, Yoshiaki; Kanamori, Takashi; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

    2016-01-01

    5-[3-(2-Aminopyrimidin-4-yl)aminopropyn-1-yl]uracil (Ura(Pyr)) was designed as a new nucleobase to recognize Ade-Thy base pair in double-stranded DNA. We successfully synthesized the dexoynucleoside phosphoramidite having Ura(Pyr) and incorporated it into triplex forming oligonucleotides (TFOs). Melting temperature analysis revealed that introduction of Ura(Pyr) into TFOs could effectively stabilize their triplex structures without loss of base recognition capabilities. PMID:26602276

  15. 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

  16. 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. PMID:26944833

  17. Minor groove site coordination of adenine by platinum group metal ions: effects on basicity, base pairing, and electronic structure.

    PubMed

    Amantia, David; Price, Clayton; Shipman, Michelle A; Elsegood, Mark R J; Clegg, William; Houlton, Andrew

    2003-05-01

    Dithioether- or diamine-tethered adenine derivatives react with Pt(II), Pd(II), and Rh(III) ions to give N3-coordinated complexes of the types [MCl(SSN)](+) (M = Pt or Pd), [RhCl(3)(SSN)], or [RhCl(3)(NNN)] (where SSN = 1-(N9-adenine)-3,6-dithia-heptane or 1-(N9-adenine)-4,7-dithia-octane; NNN = ethylenediamine-N,9-ethyladenine). Single-crystal X-ray analysis confirms the nature of the metal-nucleobase interaction and highlights a conserved intermolecular hydrogen-bonding motif for all the complexes, irrespective of the metal-ion geometry. Coordination significantly reduces the basicity of the adeninyl group, as indicated by a pK(a) value of -0.16 for [PtCl(N3-1-(N9-adenine)-3,6-dithia-heptane)]BF(4), compared to a pK(a) value of 4.2 for 9-ethyladenine. The site of proton binding, N1 or N7, could not be unambiguously assigned from the (1)H NMR data, because of the similar effect on the chemical shifts of the H2 and H8 protons. Density functional calculations at the BP-LACVP level suggest N1 as the site of protonation for this type of complex. This is in contrast to the N7-protonation reported for [Pt(dien)(N3-6,6',9-trimethyladenine)](2+), as reported elsewhere (Meiser et al., Chem.-Eur. J. 1997, 3, 388). However, further electronic structure calculations in the gas phase reveal that the preferred site for protonation for N3-bound complexes is conformationally dependent. N3 coordination was also found to reduce the extent of base pairing between adenine and thymine in dimethylsulfoxide for the self-complementary complex [PtCl(L3)](+) (L3 = 1-(N9-adenine)-3,6-dithia-9-(N1-thymine)nonane), compared to that for the uncomplexed ligand. PMID:12716200

  18. 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

  19. 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.

  20. 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.

  1. Ion pair-based liquid-phase microextraction combined with cuvetteless UV-vis micro-spectrophotometry as a miniaturized assay for monitoring ammonia in waters.

    PubMed

    Senra-Ferreiro, Sonia; Pena-Pereira, Francisco; Costas-Mora, Isabel; Romero, Vanesa; Lavilla, Isela; Bendicho, Carlos

    2011-09-15

    A miniaturized method based on liquid-phase microextraction (LPME) in combination with microvolume UV-vis spectrophotometry for monitoring ammonia in waters is proposed. The methodology is based on the extraction of the ion pair formed between the blue indophenol obtained according to the Berthelot reaction and a quaternary ammonium salt into a microvolume of organic solvent. Experimental parameters affecting the LPME performance such as type and concentration of the quaternary ammonium ion salt required to form the ion pair, type and volume of extractant solvent, effect of disperser solvent, ionic strength and extraction time, were optimized. A detection limit of 5.0 μg L(-1) ammonia and an enrichment factor of 30 can be attained after a microextraction time of 4 min. The repeatability, expressed as relative standard deviation, was 7.6% (n=7). The proposed method can be successfully applied to the determination of trace amounts of ammonia in several environmental water samples. PMID:21807208

  2. 5-Methylation of Cytosine in CG:CG Base-pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics

    PubMed Central

    Yusufaly, Tahir I.; Li, Yun; Olson, Wilma K.

    2014-01-01

    Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile ‘opening’ mode and two shear ‘sliding’ and ‘tearing’ modes in the orthogonal plane. The stacking interactions of the methyl groups globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. Additionally, the indirect effects of the methyl groups on possible base-pair steps neighboring CG:CG are observed to be of comparable importance to their direct effects on CG:CG. The results have implications for the epigenetic control of DNA mechanics. PMID:24313757

  3. The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli

    PubMed Central

    Beisel, Chase L.; Storz, Gisela

    2011-01-01

    SUMMARY Bacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse non-preferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multi-output feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression. PMID:21292161

  4. 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

  5. 43 CFR 420.3 - Adjacent lands.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 1 2014-10-01 2014-10-01 false Adjacent lands. 420.3 Section 420.3 Public Lands: Interior Regulations Relating to Public Lands BUREAU OF RECLAMATION, DEPARTMENT OF THE INTERIOR...-managing agencies on adjacent lands (both public and private)....

  6. 43 CFR 420.3 - Adjacent lands.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 1 2013-10-01 2013-10-01 false Adjacent lands. 420.3 Section 420.3 Public Lands: Interior Regulations Relating to Public Lands BUREAU OF RECLAMATION, DEPARTMENT OF THE INTERIOR...-managing agencies on adjacent lands (both public and private)....

  7. 43 CFR 420.3 - Adjacent lands.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Adjacent lands. 420.3 Section 420.3 Public Lands: Interior Regulations Relating to Public Lands BUREAU OF RECLAMATION, DEPARTMENT OF THE INTERIOR OFF-ROAD VEHICLE USE § 420.3 Adjacent lands. When administratively feasible, the regulation of off-road vehicle use on Reclamation lands will...

  8. 43 CFR 420.3 - Adjacent lands.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true Adjacent lands. 420.3 Section 420.3 Public Lands: Interior Regulations Relating to Public Lands BUREAU OF RECLAMATION, DEPARTMENT OF THE INTERIOR...-managing agencies on adjacent lands (both public and private)....

  9. 43 CFR 420.3 - Adjacent lands.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Adjacent lands. 420.3 Section 420.3 Public Lands: Interior Regulations Relating to Public Lands BUREAU OF RECLAMATION, DEPARTMENT OF THE INTERIOR OFF-ROAD VEHICLE USE § 420.3 Adjacent lands. When administratively feasible, the regulation of...

  10. DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental-Theoretical Case Study of the AT Homo-Oligonucleotide.

    PubMed

    Di Meo, Florent; Pedersen, Morten N; Rubio-Magnieto, Jenifer; Surin, Mathieu; Linares, Mathieu; Norman, Patrick

    2015-02-01

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment. PMID:26261947

  11. 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

  12. Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion.

    PubMed

    Chen, Yongheng; Zhang, Xiaojun; Dantas Machado, Ana Carolina; Ding, Yuan; Chen, Zhuchu; Qin, Peter Z; Rohs, Remo; Chen, Lin

    2013-09-01

    The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood. Here we describe the crystal structure of the p53 core domain bound to a naturally occurring RE located at the promoter of the Bcl-2-associated X protein (BAX) gene, which contains a one base-pair insertion between the two half-sites. Surprisingly, p53 forms a tetramer on the BAX-RE that is nearly identical to what has been reported on other REs with a 0-bp spacer. Each p53 dimer of the tetramer binds in register to a half-site and maintains the same protein-DNA interactions as previously observed, and the two dimers retain all the protein-protein contacts without undergoing rotation or translation. To accommodate the additional base pair, the DNA is deformed and partially disordered around the spacer region, resulting in an apparent unwinding and compression, such that the interactions between the dimers are maintained. Furthermore, DNA deformation within the p53-bound BAX-RE is confirmed in solution by site-directed spin labeling measurements. Our results provide a structural insight into the mechanism by which p53 binds to discontinuous sites with one base-pair spacer. PMID:23836939

  13. 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

  14. Anomalous scaling of Δ C versus T c in the Fe-based superconductors: the $${S}_{\\pm }$$-wave pairing state model

    DOE PAGESBeta

    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

  15. 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.

  16. 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

  17. 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

  18. Fiber-based photon-pair source capable of hybrid entanglement in frequency and transverse mode, controllably scalable to higher dimensions

    NASA Astrophysics Data System (ADS)

    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.

    2016-06-01

    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.

  19. 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

  20. 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.

  1. Pairing of weakly correlated electrons in the platinum-based centrosymmetric superconductor SrPt3P

    NASA Astrophysics Data System (ADS)

    Shiroka, T.; Pikulski, M.; Zhigadlo, N. D.; Batlogg, B.; Mesot, J.; Ott, H.-R.

    2015-06-01

    We report a study of the normal- and superconducting-state electronic properties of the centrosymmetric compound SrPt3P via 31P nuclear-magnetic-resonance (NMR) and magnetometry investigations. Essential features such as a sharp drop of the Knight shift at T pairing in SrPt3P , although a direct confirmation in the form of a Hebel-Slichter-type peak is lacking. Normal-state NMR data at T <50 K indicate conventional features of the conduction electrons, typical of simple metals such as lithium or silver. Our data are finally compared with available NMR results for the noncentrosymmetric superconductors LaPt3Si and CePt3Si , which adopt similar crystal structures.

  2. 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.

  3. 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.

  4. 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

  5. Solvation of deoxynucleosides in aqueous mixtures of organic solvents probed through their intrinsic fluorescence: Implications for open base pair states in DNA

    NASA Astrophysics Data System (ADS)

    Ababneh, Anas Mohammad

    Because of the importance of solvation in the function of DNA, there is considerable interest in understanding the solvation network of its constituent components. This is of particular importance in connection with the closing of base pairs that have been disrupted as a result of structural fluctuations. Following the opening of a base pair, the open base is exposed to a heterogeneous environment which involves polar as well as nonpolar interactions. Toward the goal of understanding how the open bases interact with such a heterogeneous environment, we have studied the intrinsic fluorescence properties of the purine and pyrimidine nucleosides (dG, dA, dT, and dC) in organic solvents in the presence of small amounts of water. Exposure of the nucleoside to water was done by preparing solutions in three different ways: (i) "premixed" solution in which the nucleoside is dissolved in a water-organic solvent mixture, (ii) "carry its own water" solution in which the nucleoside is first dissolved in water and then diluted in the organic solvent, and (iii) "injected" solution in which water is added to a solution of the nucleoside in the organic solvent. The organic solvents used in the present study were: n-butanol, acetonitrile, methanol, n-propanol, isopropanol, and isobutanol. We find that for n-butanol and acetonitrile, which have a high degree of amphiphilicity and weak hydrogen bonding ability, respectively, the fluorescence spectral properties of the purines are found to depend on the sequence of the steps in which the aqueous mixture was formed. By contrast, no such dependence was observed in the other organic solvents. On the other hand, no such dependence was observed for the pyrimidines in any of the organic solvents used in the present study. These findings suggest that the final solvation network around the purines is dependent on the nature of the environment to which they were initially exposed. This would tend to present an impediment to the closing of

  6. 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

  7. 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

  8. 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.

  9. A Tester System for Detecting Each of the Six Base-Pair Substitutions in Saccharomyces Cerevisiae by Selecting for an Essential Cysteine in Iso-1-Cytochrome C

    PubMed Central

    Hampsey, M.

    1991-01-01

    A collection of isogenic yeast strains that is specifically diagnostic for the six possible base-pair substitutions is described. Each strain contains a single, unique base-pair substitution at the Cys-22 codon of the CYC1 gene, which codes for iso-1-cytochrome c. These mutations encode replacements of the functionally critical Cys-22 and render each strain unable to grow on media containing nonfermentable carbon sources (Cyc(-)). Specific base-pair substitutions, which restore the Cys-22 codon, can be monitored simply by scoring for reversion to the Cyc(+) phenotype. These strains revert spontaneously at very low frequencies and exhibit specific patterns of reversion in response to different mutagens. Only true (CYC1(+)) revertants were recovered after 7 days on selection medium. The following mutagen specificities were observed: ethyl methanesulfonate and N-methyl-N'-nitro-N-nitrosoguanidine, G.C -> A.T; 4-nitroquinoline-1-oxide, G.C -> T.A and G.C -> A.T; diepoxybutane, A.T -> T.A, A.T -> G.C and G.C -> T.A; 5-azacytidine, G.C -> C.G. Methyl methanesulfonate induced all six mutations, albeit at relatively low frequencies, with preference for A.T -> T.A and A.T -> G.C. Ultraviolet light was the most inefficient mutagen used in this study, consistent with its preference for transition mutations at dipyrimidine sequences reported in other systems. This tester system is valuable as a simple and reliable assay for specific mutations without DNA sequence analysis. PMID:1648005

  10. 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. PMID:24529944

  11. On the conditions for enhanced transport through molecular junctions based on metal centres ligated by pairs of pyridazino-derived ligands

    SciTech Connect

    Ding, Bei; Washington, Victoria; Dunietz, Barry D

    2010-10-10

    Transport properties of a Ni bis-η{sup 2} complex ligated by a pair of bi-pyridazino derivative are considered. This complex provides the opportunity to avoid perpendicular alignment of the ligand π planes. We study the effects of π-bonding and of intramolecular hydrogen bonding between the ligands as mediated by the metal centre on electron transport. The complicated effect of the electronic structure equilibration with the electrodes on the transport is discussed. The analysis at the electronic structure level provides guidelines to design a molecular bridge that is based on metal complexation with effective electronic transport.

  12. 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.

  13. Four-Wave Mixing Crosstalk Suppression Based on the Pairing Combinations of Differently Linear-Polarized Optical Signals

    PubMed Central

    Abd, Haider; Din, Norashidah Md.; Al-Mansoori, M. H.; Abdullah, F.; Fadhil, H. A.

    2014-01-01

    A new approach to suppressing the four-wave mixing (FWM) crosstalk by using the pairing combinations of differently linear-polarized optical signals was investigated. The simulation was conducted using a four-channel system, and the total data rate was 40 Gb/s. A comparative study on the suppression of FWM for existing and suggested techniques was conducted by varying the input power from 2 dBm to 14 dBm. The robustness of the proposed technique was examined with two types of optical fiber, namely, single-mode fiber (SMF) and dispersion-shifted fiber (DSF). The FWM power drastically reduced to less than −68 and −25 dBm at an input power of 14 dBm, when the polarization technique was conducted for SMF and DSF, respectively. With the conventional method, the FWM powers were, respectively, −56 and −20 dBm. The system performance greatly improved with the proposed polarization approach, where the bit error rates (BERs) at the first channel were 2.57 × 10−40 and 3.47 × 10−29 at received powers of −4.90 and −13.84 dBm for SMF and DSF, respectively. PMID:24883364

  14. 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

  15. 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

  16. 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

  17. 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

  18. Surface finish quality of the outer AXAF mirror pair based on X-ray measurements of the VETA-I

    NASA Technical Reports Server (NTRS)

    Hughes, John P.; Schwartz, Daniel; Szentgyorgyi, Andrew; Van Speybroeck, Leon; Zhao, Ping

    1993-01-01

    We employ the X-ray measurements of the VETA-I taken at the X-Ray Calibration Facility (XRCF) of the Marshall Space Flight Center (MSFC) to extract information about the surface finish quality of the outermost pair of AXAF mirrors. The particular measurements we consider are 1D scans of the core of the point response function (PRF) (FWHM scans), the encircled energy as a function of radius, and 1D scans of the wings of the PRF. We discuss briefly our raytrace model which incorporates the numerous effects present in the VETA-I test, such as the finite source distance, the size and shape of the X-ray source, the residual gravitational distortions of the optic, the despace of the VETA-I, and particulate contamination. We show how the data constrain the amplitude of mirror surface deviations for spatial frequencies greater than about 0.1/mm. Constraints on the average amplitude of circumferential slope errors are derived as well.

  19. Surface finish quality of the outer AXAF mirror pair based on x ray measurements of the VETA-I

    NASA Technical Reports Server (NTRS)

    Hughes, John P.; Schwartz, Daniel A.; Szentgyorgyi, Andrew; Vanspeybroeck, Leon; Zhao, Ping

    1992-01-01

    We employ the X-ray measurements of the VETA-I taken at the X-Ray Calibration Facility (XRCF) of the Marshall Space Flight Center (MSFC) to extract information about the surface finish quality of the outermost pair of AXAF mirrors. The particular measurements we consider are one dimensional scans of the core of the point response function (PRF) (full width half maximum (FWHM) scans), the encircled energy as a function of radius, and one dimensional scans of the wings of the PRF. We discuss briefly our ray trace model which incorporates the numerous effects present in the VETA-I test, such as the finite source distance, the size and shape of the X-ray source, the residual gravitational distortions of the optic, the despace of the VETA-I, and particulate contamination. We show how the data constrain the amplitude of mirror surface deviations for spatial frequencies greater than about 0.1 mm(exp -1). Constraints on the average amplitude of circumferential slope errors are derived as well.

  20. 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.

  1. 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.

  2. 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

  3. A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing

    PubMed Central

    Kim, Pan-Gyu; Cho, Hwan-Gue; Park, Kiejung

    2008-01-01

    We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures. PMID:18414585

  4. 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. PMID:25904704

  5. 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.

  6. 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.

  7. Epstein-Barr virus-associated persistent polyclonal B-cell lymphocytosis with a distinct 69-base pair deletion in the LMP1 oncogene.

    PubMed

    Larcher, C; McQuain, C; Berger, C; Mitterer, M; Quesenberry, P J; Huemer, H P; Knecht, H

    1997-01-01

    Epstein-Barr virus (EBV) genomes have been detected in peripheral blood lymphocytes (PBL) of patients with persistent polyclonal B-cell lymphocytosis (PPBL). This is consistent with the hypothesis that latent EBV infection is involved in the pathogenesis of this disorder. Two EBV-encoded proteins expressed in viral latency are the latent membrane proteins 1 and 2A (LMP1 and LMP2A). We have studied the LMP1 oncogene and the LMP2A gene in a female patient with PPBL and her five siblings. A cell line derived from peripheral blood lymphocytes (PBL) of the patient was also analyzed. A distinct 69-base pair deletion was identified within the carboxy terminal NF-kappa B activation domain of the LMP1 oncogene in PBL of the patient and in the cell line, whereas none of the siblings harbored this deletion. The tyrosine-signaling motif and the HLA A2.1 epitope of the LMP2A gene were wild type in the patient and all siblings. The presence of a 69-base pair deletion variant of the LMP1 oncogene within the lymphocytes of a PPBL patient but absence of this deletion variant in the unaffected siblings suggests a direct implication of altered LMP1 oncoprotein-dependent function in the pathogenesis of PPBL. PMID:9031611

  8. 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.

  9. Expression of a gene in a 400-base-pair fragment of colicin plasmid ColE2-P9 is sufficient to cause host cell lysis.

    PubMed Central

    Pugsley, A P; Schwartz, M

    1983-01-01

    The colicin E2 immunity (ceiB) and lysis (celB) genes of colicin plasmid ColE2-P9 were cloned as a 900-base-pair insert under the control of the lac promoter in high-copy-number plasmid pUR222. Hosts carrying this plasmid were immune to colicin E2, produced increased amounts of immunity protein (molecular weight, 9,000) and two smaller proteins (molecular weights, 5,000 and 3,000), and lysed when incubated in medium containing isopropyl-beta-D-thiogalactopyranoside (IPTG). A 400-base-pair lacp-distal fragment derived from the insert in this plasmid was recloned in the same orientation into pUR222. Although hosts carrying this plasmid also lysed when grown in the presence of IPTG, they were sensitive to colicin E2 and produced increased amounts of the 5,000- and 3,000-molecular-weight proteins (but not the full-length immunity protein) when treated with IPTG. The results were consistent with the idea that expression of celB (production of the 5,000- and 3,000-molecular-weight proteins) is sufficient to cause host cell lysis in the absence of colicin production and derepression of the host cell SOS system. Images PMID:6352670

  10. 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

  11. 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.

  12. 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

  13. SOLIDS TRANSPORT BETWEEN ADJACENT CAFB FLUIDIZED BEDS

    EPA Science Inventory

    The report gives results of an experimental investigation of a pulsed, dense-phase pneumatic transport system for controlled circulation between adjacent fluidized beds. A model was developed to predict performance. The program provides technical support for EPA's program to demo...

  14. Border separation for adjacent orthogonal fields

    SciTech Connect

    Werner, B.L.; Khan, F.M.; Sharma, S.C.; Lee, C.K.; Kim, T.H. )

    1991-06-01

    Field border separations for adjacent orthogonal fields can be calculated geometrically, given the validity of some important assumptions such as beam alignment and field uniformity. Thermoluminescent dosimetry (TLD) measurements were used to investigate dose uniformity across field junctions as a function of field separation and, in particular, to review the CCSG recommendation for the treatment of medulloblastoma with separate head and spine fields.

  15. 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).

  16. 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

  17. 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

  18. 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

  19. Reconstitution of a functional IS608 single-strand transpososome: role of non-canonical base pairing.

    PubMed

    He, Susu; Hickman, Alison B; Dyda, Fred; Johnson, Neil P; Chandler, Michael; Ton-Hoang, Bao

    2011-10-01

    Single-stranded (ss) transposition, a recently identified mechanism adopted by members of the widespread IS200/IS605 family of insertion sequences (IS), is catalysed by the transposase, TnpA. The transposase of IS608, recognizes subterminal imperfect palindromes (IP) at both IS ends and cleaves at sites located at some distance. The cleavage sites, C, are not recognized directly by the protein but by short sequences 5' to the foot of each IP, guide (G) sequences, using a network of canonical ('Watson-Crick') base interactions. In addition a set of non-canonical base interactions similar to those found in RNA structures are also involved. We have reconstituted a biologically relevant complex, the transpososome, including both left and right ends and TnpA, which catalyses excision of a ss DNA circle intermediate. We provide a detailed picture of the way in which the IS608 transpososome is assembled and demonstrate that both C and G sequences are essential for forming a robust transpososome detectable by EMSA. We also address several questions central to the organization and function of the ss transpososome and demonstrate the essential role of non-canonical base interactions in the IS608 ends for its stability by using point mutations which destroy individual non-canonical base interactions. PMID:21745812

  20. The Taili-Yiwulüshan metamorphic core complex corridor: Diachronous exhumation and relationships to the adjacent basins based on new 40Ar/39Ar and (U-Th-Sm)/He mineral ages

    NASA Astrophysics Data System (ADS)

    Liang, Chenyue; Neubauer, Franz; Liu, Yongjiang; Genser, Johann; Dunkl, István; Heberer, Bianca; Jin, Wei; Zeng, Zuoxun; Li, Weimin; Wen, Quanbo; Li, Jing

    2015-04-01

    The Xingcheng-Taili ductile shear zone (western Liaoning Province in China) formed during latest Jurassic to Early Cretaceous crustal extension of the eastern North China craton, and exhumed low to medium metamorphic grade Archean, Upper Triassic and Upper Jurassic granitic rocks. The Mesozoic Yiwulüshan metamorphic core complex (Yiwulüshan MCC) is dominated by a NNE-SSW elongated dome with a left-lateral shear zone, which is located in the northeastern part of Xingcheng-Taili ductile shear zone, and combine as Taili-Yiwulüshan metamorphic core complex corridor. To the east, it is bounded by the NNE-trending Cretaceous to Eocene Liaohe basin (the northern extension of the Bohai Bay basin), and to the west by the Cretaceous-aged Fuxin-Yixian basin, which could potentially interpreted as supra-detachment basins. Here, we present results from a multi-method thermochronological study and coupled with structural investigations and sections of adjacent supra-detachment basins, which constrain the timing of regional deformation as well as the cooling history and exhumation processes of the low- to middle-grade metamorphic complex in the Taili-Yiwulüshan MCC corridor, in order to understand the mode of lithospheric scale reactivation, extension and thinning of the North China craton. The new40Ar/39Ar muscovite, biotite, K-feldspar and (U-Th)/He apatite ages from granitic rocks help constrain the thermal evolution during its exhumation. The thermochronologic studies have shown at least three stages of exhumation and cooling from late Jurassic to Eocene in Xingcheng-Taili shear zone should be distinguished, e.g., ~ 150-130 Ma, 130-115 Ma and 115-52 Ma, respectively. Diachronous onset and subsequent parallel cooling and exhumation characterize the early thermal history. The Yiwulüshan MCC has a similar exhumation history from 135 to 97 Ma with a similar cooling history. The development of Taili-Yiwulüshan MCC corridor is associated with synkinematic emplacement

  1. 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.

  2. C. Y. Chao, Pair Creation and Pair Annihilation

    NASA Astrophysics Data System (ADS)

    Li, Bing An; Yang, C. N.

    C. Y. Chao's contribution to physicists' acceptance of QED in 1933-1934 through his experiments of 1930 is analyzed. It is pointed out that Blackett and Occhialini's key suggestion of 1933 about hole theory was based on identifying Chao's "additional scattered rays" (1930) as due to pair annihilation.

  3. C. Y. Chao, Pair Creation and Pair Annihilation

    NASA Astrophysics Data System (ADS)

    Li, Bing An; Yang, C. N.

    2013-05-01

    C. Y. Chao's contribution to physicists' acceptance of QED in 1933-1934 through his experiments of 1930 is analyzed. It is pointed out that Blackett and Occhialini's key suggestion of 1933 about hole theory was based on identifying Chao's "additional scattered rays" (1930) as due to pair annihilation.

  4. Iterated combination-based paired permutation tests to determine shape effects of chemotherapy in patients with esophageal cancer.

    PubMed

    Alfieri, Rita; Bonnini, Stefano; Brombin, Chiara; Castoro, Carlo; Salmaso, Luigi

    2016-04-01

    The nonparametric combination of dependent permutation tests method is a useful general tool when a testing problem can be broken down into a set of different k > 1 partial tests. These partial tests, after adjustment of p-values to control for multiplicity, can be marginally analyzed, but jointly considered they can provide information on an overall hypothesis, which might represent the true goal of the testing problem. On the one hand, independence among the partial tests is usually an unrealistic assumption; on the other, even when the underlying dependence relations are known quite often they are difficult to cope with properly. Therefore this combination must be achieved nonparametrically, by implicitly taking into account the dependence structure of tests without explicitly describing it. An important property of the tests based on nonparametric combination methodology, when the number of response variables is high compared to the sample sizes, consists in the finite sample consistency. A practical problem involves choosing the most suitable combining function for each specific testing problem given that the final result can be affected by this crucial choice. The purpose of this article is to present an nonparametric combination solution based on the iterated combination of partial tests, evaluate its power behavior using a Monte Carlo simulation study and apply it to a real medical problem, namely the evaluation of the effects of chemotherapy on the shape of esophageal tumors. R code has been implemented to carry out the analyses. PMID:23070597

  5. The simian varicella virus genome contains an invertible 665 base pair terminal element that is absent in the varicella zoster virus genome

    PubMed Central

    Mahalingam, Ravi; Gray, Wayne L.

    2007-01-01

    Simian varicella virus (SVV) causes chickenpox in monkeys, establishes latency, and reactivates to produce zoster thus providing a model to study human varicella zoster virus (VZV) infection. Sequence analysis of a recombinant cosmid clone containing the left end of the SVV genome revealed a 665 base pair (bp) segment that is absent in VZV DNA. This segment inverts and contains 507 bp of unique sequences flanked on either side by 79 bp inverted repeats, making the SVV genome to be 124,785 bp in size. Part of the inverted repeat sequence (64 bp) is also present at the junction of the long and short segments of the SVV genome. The terminal DNA sequences are conserved among different SVV isolates and present in tissues from infected monkeys. The terminal region is transcriptionally active and is also present in the genomes of other animal varicelloviruses, but absent in the VZV genome. PMID:17555785

  6. 5-Methylation of Cytosine in CG:CG Base-Pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics

    NASA Astrophysics Data System (ADS)

    Yusufaly, Tahir; Olson, Wilma; Li, Yun

    2014-03-01

    Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile ``opening'' mode and two shear ``sliding'' and ``tearing'' modes in the orthogonal plane. The stacking interactions of the methyl groups are observed to globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. The results have implications for the epigenetic control of DNA mechanics.

  7. 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.

  8. 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

  9. 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

  10. 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. PMID:24012890

  11. 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. PMID:19715282

  12. 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

  13. REH2C Helicase and GRBC Subcomplexes May Base Pair through mRNA and Small Guide RNA in Kinetoplastid Editosomes.

    PubMed

    Kumar, Vikas; Madina, Bhaskara R; Gulati, Shelly; Vashisht, Ajay A; Kanyumbu, Chiedza; Pieters, Brittany; Shakir, Afzal; Wohlschlegel, James A; Read, Laurie K; Mooers, Blaine H M; Cruz-Reyes, Jorge

    2016-03-11

    Mitochondrial mRNAs in Trypanosoma brucei undergo extensive insertion and deletion of uridylates that are catalyzed by the RNA editing core complex (RECC) and directed by hundreds of small guide RNAs (gRNAs) that base pair with mRNA. RECC is largely RNA-free, and accessory mitochondrial RNA-binding complex 1 (MRB1) variants serve as scaffolds for the assembly of mRNA-gRNA hybrids and RECC. However, the molecular steps that create higher-order holoenzymes ("editosomes") are unknown. Previously, we identified an RNA editing helicase 2-associated subcomplex (REH2C) and showed that REH2 binds RNA. Here we showed that REH2C is an mRNA-associated ribonucleoprotein (mRNP) subcomplex with editing substrates, intermediates, and products. We isolated this mRNP from mitochondria lacking gRNA-bound RNP (gRNP) subcomplexes and identified REH2-associated cofactors 1 and 2 ((H2)F1 and (H2)F2). (H2)F1 is an octa-zinc finger protein required for mRNP-gRNP docking, pre-mRNA and RECC loading, and RNP formation with a short synthetic RNA duplex. REH2 and other eukaryotic DEAH/RHA-type helicases share a conserved regulatory C-terminal domain cluster that includes an oligonucleotide-binding fold. Recombinant REH2 and (H2)F1 constructs associate in a purified complex in vitro. We propose a model of stepwise editosome assembly that entails controlled docking of mRNP and gRNP modules via specific base pairing between their respective mRNA and gRNA cargo and regulatory REH2 and (H2)F1 subunits of the novel mRNP that may control specificity checkpoints in the editing pathway. PMID:26769962

  14. 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

  15. 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.

  16. 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.

  17. Unique TTC Repeat Base Pair Loss Mutation In Cases of Pure Neural Leprosy: A Survival Strategy of Mycobacterium Leprae?

    PubMed Central

    De, Abhishek; Reja, Abu Hena Hasanoor; Biswas, Supratik; Bhattacharya, Basudev; Chatterjee, Gobinda; Basu, Keya; Sarda, Aarti; Chowdhury, Nidhi

    2015-01-01

    Background: Genomic reduction helps obligate intracellular microbes to survive difficult host niches. Adaptation of Mycobacterium leprae in cases of pure neural leprosy (PNL) in the intracellular niche of peripheral nerves can be associated with some gene loss. Recently, a stable but variable number of tandem repefzats (TTC) have been reported in strains of M. leprae. FolP and rpoB genes are the two common mutation sites which deal with the susceptibility of the bacteria to drugs. Aim: We attempted to find if genomic reduction of M. leprae in context of these TTC repeats or mutations in folP1 and rpoB can be the reason for the restriction of M. leprae in the nerves in PNL. Materials and Methods: DNA extracts taken from fine needle aspiration of affected nerves of 24 PNL cases were studied for tandem repeats with 21TTC primer in multiplex-PCR. Mutations were also studied by PCR Amplification of SRDR (Sulphone Resistance Determining Region) of the folP1 and multiple primer PCR amplification refractory mutation system (MARS) of the rpoB. Results: Of the 24 PNL, only 1 patient showed mutation in the rpoB gene and none in the folp1 gene. Studying the mutation in TTC region of the M. leprae gene we found that all the cases have a loss of a few bases in the sequence. Conclusion: We can conclude that there is consistent loss in the bases in the TTC region in all cases of pure neural Hansen and we postulate that it may be an adaptive response of the bacteria to survive host niche resulting in its restriction to peripheral nerves. PMID:26288401

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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. PMID:19204118

  3. 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

  4. 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. PMID:27340541

  5. 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.

  6. Invisibly Sanitizable Signature without Pairings

    NASA Astrophysics Data System (ADS)

    Yum, Dae Hyun; Lee, Pil Joong

    Sanitizable signatures allow sanitizers to delete some pre-determined parts of a signed document without invalidating the signature. While ordinary sanitizable signatures allow verifiers to know how many subdocuments have been sanitized, invisibly sanitizable signatures do not leave any clue to the sanitized subdocuments; verifiers do not know whether or not sanitizing has been performed. Previous invisibly sanitizable signature scheme was constructed based on aggregate signature with pairings. In this article, we present the first invisibly sanitizable signature without using pairings. Our proposed scheme is secure under the RSA assumption.

  7. Nucleon pairing in Sn isotopes

    NASA Astrophysics Data System (ADS)

    Imasheva, L.; Ishkhanov, B.; Stepanov, M.; Tretyakova, T.

    2016-01-01

    The systematics of excited states in Sn isotopes are discussed on basis of pairing interaction in nuclei. Nucleon paring leads to formation of excited states multiplets. The estimation of multiplet splitting based on experimental nuclear masses allows one to calculate the position of excited states with different seniority in δ-approximation. The wide systematics of the spectra of Sn isotopes gives a possibility to check the pairing interaction for different subshells and consider the multiplets of excited states in the neutron-rich isotopes far from stability.

  8. Stereo pairs from linear morphing

    NASA Astrophysics Data System (ADS)

    McAllister, David F.

    1998-04-01

    Several authors have recently investigated the ability to compute intermediate views of a scene using given 2D images from arbitrary camera positions. The methods fall under the topic of image based rendering. In the case we give here, linear morphing between two parallel views of a scene produces intermediate views that would have been produced by parallel movement of a camera. Hence, the technique produces images computed in a way that is consistent with the standard off-axis perspective projection method for computing stereo pairs. Using available commercial 2D morphing software, linear morphing can be used to produce stereo pairs from a single image with bilateral symmetry such as a human face. In our case, the second image is produced by horizontal reflection. We describe morphing and show how it can be used to provide stereo pairs from single images.

  9. A school-based rope skipping intervention for adolescents in Hong Kong: protocol of a matched-pair cluster randomized controlled trial

    PubMed Central

    2014-01-01

    Background Schools present venues for physical activity promotion among youth, with physical education (PE) considered the primary vehicle responsible for increasing activity levels. Yet students are not very physically active during typical school PE classes. With the aim to engage Hong Kong students in more moderate-to-vigorous physical activity (MVPA) during PE, a fitness infusion intervention using rope skipping was designed, and its effectiveness will be examined. Rope skipping was chosen because a) it provides moderate-to-high intensity physical activity; b) is inexpensive; c) students find it enjoyable; and d) is feasible in typical environments in Hong Kong, where PE classes are large in size (up to 40 students) and space available for physical activity is usually limited. Methods/Design A matched-pair cluster randomized controlled trial was designed. Secondary school students from 24 classes (from 12 schools) will be recruited to participate in the trial. Students’ baseline MVPA will be measured during school PE. Classes will be matched according to baseline variables and one class from each pair will be randomized into the experimental group. Teachers in the experimental group will be invited to attend a teacher workshop, and will insert a 15-minute rope skipping activity in four consecutive PE lessons. Motivational factors based on self-determination theory will also be measured as secondary outcomes. The effectiveness of the intervention will be evaluated by comparing changes in the proportion of lesson time spent in MVPA from baseline to follow-up across the experimental and control groups. Discussion Physical activity levels in PE are often very low and there is a need to identify feasible low-cost interventions that can be easily disseminated. If the results of the study suggest the intervention to be effective, it could be implemented to schools throughout Hong Kong and other cities where space is limited. Trail registration ANZCTR: ACTRN

  10. 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

  11. Formation of N-N cross-links in DNA by reaction of radiation-produced DNA base pair diradicals: a DFT study.

    PubMed

    Pottiboyina, Venkata; Kumar, Anil; Sevilla, Michael D

    2011-12-22

    This study employs DFT (density functional theory) to investigate the formation of hydrazine-like (N-N) cross-linked structures between DNA base pair diradicals that are likely to result from the interaction of high linear energy transfer (LET) radiation, such as ion-beam radiation, with DNA. In our calculations, we generated the guanine (G), cytosine (C), adenine (A), and thymine (T) radicals by removing one hydrogen atom from an N-H bond involved in the normal base pairing. The radical species formed are those that naturally result from one-electron oxidation of the bases followed by deprotonation. N-N cross-links between G and C or A and T diradicals were studied using the BHandHLYP, B3LYP, M06, and M06-2X density functionals and 6-31G* basis set. From a comparison to several test cases performed with the G3B3 method, which gives thermodynamically reliable values, we found that calculations employing the BHandHLYP/6-31G* method predict the best estimates of bonding energies for hydrazine-like structures. Our study shows that the N-N cross-link formed between guanine radical and a neutral cytosine is endothermic in nature but can form metastable structures. However, the reactions between two DNA base radicals (diradical) to form several N-N cross-linked structures are found to be highly exothermic in nature. The N-N cross-links formed between various G-C, G-G, and C-C diradicals have binding energies in the range of ca. -54 to -68, -41 to -47, and -67 to -75 kcal/mol, respectively, whereas A-T, A-A, and T-T have binding energies of -80, -60, and -98 kcal/mol, respectively. In all purine-pyrimidine N-N cross-linked structures, the highest occupied molecular orbital (HOMO) is found to be localized on the purine moiety and the lowest unoccupied molecular orbital (LUMO) is on the pyrimidine moiety. PMID:22050209

  12. Critical Schwinger Pair Production

    NASA Astrophysics Data System (ADS)

    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.

  13. 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

  14. Cooper Pairs in Insulators?!

    ScienceCinema

    James Valles

    2010-01-08

    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. 

  15. 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.

  16. Frustrated Lewis Pairs.

    PubMed

    Stephan, Douglas W

    2015-08-19

    The articulation of the notion of "frustrated Lewis pairs" (FLPs), which emerged from the discovery that H2 can be reversibly activated by combinations of sterically encumbered Lewis acids and bases, has prompted a great deal of recent activity. Perhaps the most remarkable consequence has been the development of FLP catalysts for the hydrogenation of a range of organic substrates. In the past 9 years, the substrate scope has evolved from bulky polar species to include a wide range of unsaturated organic molecules. In addition, effective stereoselective metal-free hydrogenation catalysts have begun to emerge. The mechanism of this activation of H2 has been explored, and the nature and range of Lewis acid/base combinations capable of effecting such activation have also expanded to include a variety of non-metal species. The reactivity of FLPs with a variety of other small molecules, including olefins, alkynes, and a range of element oxides, has also been developed. Although much of this latter chemistry has uncovered unique stoichiometric transformations, metal-free catalytic hydroamination, CO2 reduction chemistry, and applications in polymerization have also been achieved. The concept is also beginning to find applications in bioinorganic and materials chemistry as well as heterogeneous catalysis. This Perspective highlights many of these developments and discusses the relationship between FLPs and established chemistry. Some of the directions and developments that are likely to emerge from FLP chemistry in the future are also presented. PMID:26214241

  17. Reconstructing genome mixtures from partial adjacencies.

    PubMed

    Mahmoody, Ahmad; Kahn, Crystal L; Raphael, Benjamin J

    2012-01-01

    Many cancer genome sequencing efforts are underway with the goal of identifying the somatic mutations that drive cancer progression. A major difficulty in these studies is that tumors are typically heterogeneous, with individual cells in a tumor having different complements of somatic mutations. However, nearly all DNA sequencing technologies sequence DNA from multiple cells, thus resulting in measurement of mutations from a mixture of genomes. Genome rearrangements are a major class of somatic mutations in many tumors, and the novel adjacencies (i.e. breakpoints) resulting from these rearrangements are readily detected from DNA sequencing reads. However, the assignment of each rearrangement, or adjacency, to an individual cancer genome in the mixture is not known. Moreover, the quantity of DNA sequence reads may be insufficient to measure all rearrangements in all genomes in the tumor. Motivated by this application, we formulate the k-minimum completion problem (k-MCP). In this problem, we aim to reconstruct k genomes derived from a single reference genome, given partial information about the adjacencies present in the mixture of these genomes. We show that the 1-MCP is solvable in linear time in the cases where: (i) the measured, incomplete genome has a single circular or linear chromosome; (ii) there are no restrictions on the chromosomal content of the measured, incomplete genome. We also show that the k-MCP problem, for k ≥ 3 in general, and the 2-MCP problem with the double-cut-and-join (DCJ) distance are NP-complete, when there are no restriction on the chromosomal structure of the measured, incomplete genome. These results lay the foundation for future algorithmic studies of the k-MCP and the application of these algorithms to real cancer sequencing data. PMID:23282028

  18. A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

    NASA Astrophysics Data System (ADS)

    Narayanaswamy, Nagarjun; Kumar, Manoj; Das, Sadhan; Sharma, Rahul; Samanta, Pralok K.; Pati, Swapan K.; Dhar, Suman K.; Kundu, Tapas K.; Govindaraju, T.

    2014-09-01

    Sequence-specific recognition of DNA by small turn-on fluorescence probes is a promising tool for bioimaging, bioanalytical and biomedical applications. Here, the authors report a novel cell-permeable and red fluorescent hemicyanine-based thiazole coumarin (TC) probe for DNA recognition, nuclear staining and cell cycle analysis. TC exhibited strong fluorescence enhancement in the presence of DNA containing AT-base pairs, but did not fluoresce with GC sequences, single-stranded DNA, RNA and proteins. The fluorescence staining of HeLa S3 and HEK 293 cells by TC followed by DNase and RNase digestion studies depicted the selective staining of DNA in the nucleus over the cytoplasmic region. Fluorescence-activated cell sorting (FACS) analysis by flow cytometry demonstrated the potential application of TC in cell cycle analysis in HEK 293 cells. Metaphase chromosome and malaria parasite DNA imaging studies further confirmed the in vivo diagnostic and therapeutic applications of probe TC. Probe TC may find multiple applications in fluorescence spectroscopy, diagnostics, bioimaging and molecular and cell biology.

  19. Efficient visible and near-infrared photoluminescent attapulgite-based lanthanide one-dimensional nanomaterials assembled by ion-pairing interactions.

    PubMed

    Xu, Jun; Zhang, Ye; Chen, Hao; Liu, Weisheng; Tang, Yu

    2014-06-01

    Attapulgite, a one-dimensional fibrillar nanomaterial present in nature, with its extreme stability, is a promising material to act as a new carrier of luminescent lanthanide complexes for further applications. Herein, a series of lanthanide complexes Na[Ln(TTA)4] have been attached to attapulgite (Atta) via ion-pairing interactions, generating the first example of attapulgite-based visible and near-infrared (NIR) luminescent lanthanide one-dimensional nanomaterials, where TTA is 2-thenoyltrifluoroacetonate and Ln is Eu, Sm, Nd, Er or Yb. The hybrid materials were characterized by CHN elemental analysis, inductively coupled plasma-atomic emission spectroscopy (ICP), powder X-ray diffraction (PXRD), thermogravimetry (TG), transmission electron microscopy (TEM), and UV-vis absorption spectra. In order to investigate the photophysical behaviours of these materials, the visible and NIR luminescent spectra and the energy transfer process have been systematically investigated. Moreover, efforts have been made to produce Eu- and Sm-based plastic attapulgite materials by utilizing poly(methyl methacrylate) (PMMA) matrices, and the dispersibility of the lanthanide-doped hybrids in PMMA provides them with a high mechanical strength. The lanthanide-doped attapulgite appears to be an interesting material for photophysical applications. The results of this work would have potential significance for the design and assembly of luminescent lanthanide materials for light-emitting diodes (LED), sunlight-conversion films, optical amplifiers, solar concentrators, and lasers. PMID:24709912

  20. Galaxy pairs align with Galactic filaments

    NASA Astrophysics Data System (ADS)

    Tempel, E.; Tamm, A.

    2015-04-01

    Context. Gravitational collapse theory and numerical simulations suggest that the velocity field within large-scale galaxy filaments is dominated by motions along the filaments. Aims: Our aim is to check whether observational data reveal any preferred orientation of galaxy pairs with respect to the underlying filaments as a result of the expectedly anisotropic velocity field. Methods: We use galaxy pairs and galaxy filaments identified from Sloan Digital Sky Survey data. For filament extraction, we use the Bisous model that is based on the marked point process technique. During the filament detection, we use the centre point of each pair instead of the positions of galaxies to avoid a built-in influence of pair orientation on the filament construction. For pairs lying within filaments (3012 cases), we calculate the angle between the line connecting the galaxies of each pair and their host filaments. To avoid redshift-space distortions, the angle is measured in the plane of the sky. Results: The alignment analysis shows that the orientation of galaxy pairs correlates strongly with their host filaments. The alignment signal is stronger for loose pairs, with at least 25% excess of aligned pairs compared to a random distribution. The alignment of galaxy pairs and filaments measured from the observational data is in good agreement with the alignment in the Millennium simulation and thus provides support to the ΛCDM formalism.