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Sample records for base analog fret-pair

  1. Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems

    DEFF Research Database (Denmark)

    Börjesson, Karl; Preus, Søren; El-Sagheer, Afaf

    2009-01-01

    We present the first nucleobase analog fluorescence resonance energy transfer (FRET)-pair. The pair consists of tCO, 1,3-diaza-2-oxophenoxazine, as an energy donor and the newly developed tC(nitro), 7-nitro-1,3-diaza-2-oxophenothiazine, as an energy acceptor. The FRET-pair successfully monitors d...

  2. In vivo dynamics of enterovirus protease revealed by fluorescence resonance emission transfer (FRET) based on a novel FRET pair

    International Nuclear Information System (INIS)

    Hsu, Y.-Y.; Liu, Y.-N.; Wang Wenyen; Kao, Fu-Jen; Kung, S.-H.

    2007-01-01

    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 2 )-peptide-red fluorescent protein 2 (DsRed2), with a cleavage motif for the enterovirus 2A protease (2A 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 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

  3. Single cell FRET analysis for the identification of optimal FRET-pairs in Bacillus subtilis using a prototype MEM-FLIM system.

    Directory of Open Access Journals (Sweden)

    Ruud G J Detert Oude Weme

    Full Text Available Protein-protein interactions can be studied in vitro, e.g. with bacterial or yeast two-hybrid systems or surface plasmon resonance. In contrast to in vitro techniques, in vivo studies of protein-protein interactions allow examination of spatial and temporal behavior of such interactions in their native environment. One approach to study protein-protein interactions in vivo is via Förster Resonance Energy Transfer (FRET. Here, FRET efficiency of selected FRET-pairs was studied at the single cell level using sensitized emission and Frequency Domain-Fluorescence Lifetime Imaging Microscopy (FD-FLIM. For FRET-FLIM, a prototype Modulated Electron-Multiplied FLIM system was used, which is, to the best of our knowledge, the first account of Frequency Domain FLIM to analyze FRET in single bacterial cells. To perform FRET-FLIM, we first determined and benchmarked the best fluorescent protein-pair for FRET in Bacillus subtilis using a novel BglBrick-compatible integration vector. We show that GFP-tagRFP is an excellent donor-acceptor pair for B. subtilis in vivo FRET studies. As a proof of concept, selected donor and acceptor fluorescent proteins were fused using a linker that contained a tobacco etch virus (TEV-protease recognition sequence. Induction of TEV-protease results in loss of FRET efficiency and increase in fluorescence lifetime. The loss of FRET efficiency after TEV induction can be followed in time in single cells via time-lapse microscopy. This work will facilitate future studies of in vivo dynamics of protein complexes in single B. subtilis cells.

  4. Branched DNA nanostructures efficiently stabilised and monitored by novel pyrene-perylene 2'-α-l-amino-LNA FRET pairs

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Santhosh Kumar, T; Campbell, Meghan A

    2013-01-01

    Novel pyrene-perylene α-l-LNA FRET pairs described herein effectively detect assembly of 2- and 3-way branched DNA nanostructures prepared by postsynthetic microwave-assisted CuAAC click chemistry. The fluorescent signalling of assembly by internally positioned FRET pairs is achieved with low...

  5. A comparison of donor-acceptor pairs for genetically encoded FRET sensors: application to the Epac cAMP sensor as an example.

    Directory of Open Access Journals (Sweden)

    Gerard N M van der Krogt

    Full Text Available We recently reported on CFP-Epac-YFP, an Epac-based single polypeptide FRET reporter to resolve cAMP levels in living cells. In this study, we compared and optimized the fluorescent protein donor/acceptor pairs for use in biosensors such as CFP-Epac-YFP. Our strategy was to prepare a wide range of constructs consisting of different donor and acceptor fluorescent proteins separated by a short linker. Constructs were expressed in HEK293 cells and tested for FRET and other relevant properties. The most promising pairs were subsequently used in an attempt to improve the FRET span of the Epac-based cAMP sensor. The results show significant albeit not perfect correlation between performance in the spacer construct and in the Epac sensor. Finally, this strategy enabled us to identify improved sensors both for detection by sensitized emission and by fluorescent lifetime imaging. The present overview should be helpful in guiding development of future FRET sensors.

  6. Josephson junction analog and quasiparticle-pair current

    DEFF Research Database (Denmark)

    Bak, Christen Kjeldahl; Pedersen, Niels Falsig

    1973-01-01

    A close analogy exists between a Josephson junction and a phase-locked loop. A new type of electrical analog based on this principle is presented. It is shown that the inclusion in this analog of a low-pass filter gives rise to a current of the same form as the Josephson quasiparticle-pair current....... A simple picture of the quasiparticle-pair current, which gives the right dependences, is obtained by assuming a junction cutoff frequency to be at the energy gap. ©1973 American Institute of Physics...

  7. Investigation of fretting corrosion of vacuum-chrome-plated vt3-1 titanium alloy in pair with unprotected vt3-1 alloy and 40khnma steel

    International Nuclear Information System (INIS)

    Rojkh, I.L.; Koltunova, L.N.; Vejtsman, M.G.; Birman, Ya.N.; Skosarev, A.V.; Kogan, I.S.

    1978-01-01

    The character of destruction of contacting surfaces in the process of fretting corrosion of titanium alloy VT3-1 chromized in vacuum in pair with unprotected alloy VT3-1 and steel 40KhNMA has been studied by scanning electron microscopy, electronography, and recording the surface profile. The specific load was 200 kg/cm 2 , vibration amplitude 50 mkm and frequency 500 Hz. It has been established that pairs unprotected with coating are subjected to intensive fretting corrosion especially when they are made of titanium alloy. For the pair chromized alloy VT3-1 - unprotected alloy VT3-1 no destruction of a chromized surface is observed. Vacuum chromium coating in the pair with steel 40KhNMA reveals similar properties as in pair with a titanium alloy. The surface of a steel sample is destroyed because of fretting corrosion, though the intensity of corrosion is lower than in the case of unprotected pairs. Vacuum chromium coating is recommended for protection of titanium alloy VT3-1 from fretting corrosion in pair with steel 40KhNMA or an alloy VT3-1 especially in those cases when various organic coatings are unsuitable

  8. Plasma analog of particle-pair production

    International Nuclear Information System (INIS)

    Tsidulko, Yu.A.; Berk, H.L.

    1996-09-01

    It is shown that the plasma axial shear flow instability satisfies the Klein-Gordon equation. The plasma instability is then shown to be analogous to spontaneous particle-pair production when a potential energy is present that is greater than twice the particle rest mass energy. Stability criteria can be inferred based on field theoretical conservation laws

  9. FRET-based modified graphene quantum dots for direct trypsin quantification in urine

    Energy Technology Data Exchange (ETDEWEB)

    Poon, Chung-Yan; Li, Qinghua [Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region (Hong Kong); Zhang, Jiali; Li, Zhongping [Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region (Hong Kong); Research Center of Environmental Science and Engineering, School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006 (China); Dong, Chuan [Research Center of Environmental Science and Engineering, School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006 (China); Lee, Albert Wai-Ming; Chan, Wing-Hong [Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region (Hong Kong); Li, Hung-Wing, E-mail: hwli@hkbu.edu.hk [Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region (Hong Kong)

    2016-04-21

    A versatile nanoprobe was developed for trypsin quantification with fluorescence resonance energy transfer (FRET). Here, fluorescence graphene quantum dot is utilized as a donor while a well-designed coumarin derivative, CMR2, as an acceptor. Moreover, bovine serum albumin (BSA), as a protein model, is not only served as a linker for the FRET pair, but also a fluorescence enhancer of the quantum dots and CMR2. In the presence of trypsin, the FRET system would be destroyed when the BSA is digested by trypsin. Thus, the emission peak of the donor is regenerated and the ratio of emission peak of donor/emission peak of acceptor increased. By the ratiometric measurement of these two emission peaks, trypsin content could be determined. The detection limit of trypsin was found to be 0.7 μg/mL, which is 0.008-fold of the average trypsin level in acute pancreatitis patient's urine suggesting a high potential for fast and low cost clinical screening. - Highlights: • A FRET-based biosensor was developed for direct quantification of trypsin. • Fast and sensitive screening of pancreatic disease was facilitated. • The direct quantification of trypsin in urine samples was demonstrated.

  10. APPL proteins FRET at the BAR: direct observation of APPL1 and APPL2 BAR domain-mediated interactions on cell membranes using FRET microscopy.

    Directory of Open Access Journals (Sweden)

    Heidi J Chial

    2010-08-01

    Full Text Available Human APPL1 and APPL2 are homologous RAB5 effectors whose binding partners include a diverse set of transmembrane receptors, signaling proteins, and phosphoinositides. APPL proteins associate dynamically with endosomal membranes and are proposed to function in endosome-mediated signaling pathways linking the cell surface to the cell nucleus. APPL proteins contain an N-terminal Bin/Amphiphysin/Rvs (BAR domain, a central pleckstrin homology (PH domain, and a C-terminal phosphotyrosine binding (PTB domain. Previous structural and biochemical studies have shown that the APPL BAR domains mediate homotypic and heterotypic APPL-APPL interactions and that the APPL1 BAR domain forms crescent-shaped dimers. Although previous studies have shown that APPL minimal BAR domains associate with curved cell membranes, direct interaction between APPL BAR domains on cell membranes in vivo has not been reported.Herein, we used a laser-scanning confocal microscope equipped with a spectral detector to carry out fluorescence resonance energy transfer (FRET experiments with cyan fluorescent protein/yellow fluorescent protein (CFP/YFP FRET donor/acceptor pairs to examine interactions between APPL minimal BAR domains at the subcellular level. This comprehensive approach enabled us to evaluate FRET levels in a single cell using three methods: sensitized emission, standard acceptor photobleaching, and sequential acceptor photobleaching. We also analyzed emission spectra to address an outstanding controversy regarding the use of CFP donor/YFP acceptor pairs in FRET acceptor photobleaching experiments, based on reports that photobleaching of YFP converts it into a CFP-like species.All three methods consistently showed significant FRET between APPL minimal BAR domain FRET pairs, indicating that they interact directly in a homotypic (i.e., APPL1-APPL1 and APPL2-APPL2 and heterotypic (i.e., APPL1-APPL2 manner on curved cell membranes. Furthermore, the results of our experiments

  11. One-step synthesis of DNA functionalized cadmium-free quantum dots and its application in FRET-based protein sensing

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Cuiling, E-mail: clzhang@chem.ecnu.edu.cn [Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241 (China); Ding, Caiping [Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241 (China); Zhou, Guohua [School of Chemistry and Chemical Engineering, Lingnan Normal University, Zhanjiang, 524048 (China); Xue, Qin [Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241 (China); Xian, Yuezhong, E-mail: yzxian@chem.ecnu.edu.cn [Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241 (China)

    2017-03-08

    DNA functionalized quantum dots (QDs) are promising nanoprobes for the fluorescence resonance energy transfer (FRET)-based biosensing. Herein, cadmium-free DNA functionalized Mn-doped ZnS (DNA-ZnS:Mn{sup 2+}) QDs were successfully synthesized by one-step route. As-synthesized QDs show excellent photo-stability with the help of PAA and DNA. Then, we constructed a novel FRET model based on the QDs and WS{sub 2} nanosheets as the energy donor-acceptor pairs, which was successfully applied for the protein detection through the terminal protection of small molecule-linked DNA assay. This work not only explores the potential bioapplication of the DNA-ZnS:Mn{sup 2+} QDs, but also provides a platform for the investigation of small molecule-protein interaction. - Highlights: • The stable and cadmium-free DNA functionalized ZnS:Mn{sup 2+} QDs were successfully synthesized through a facile one-step route. • We constructed a novel FRET system based on one-step synthesized DNA-ZnS:Mn{sup 2+} QDs (donor) and WS{sub 2} nanosheets (acceptor). • The FRET-based strategy was applied for the detection of streptavidin and folate receptor by combining TPSMLD and Exo III.

  12. rFRET: A comprehensive, Matlab-based program for analyzing intensity-based ratiometric microscopic FRET experiments.

    Science.gov (United States)

    Nagy, Peter; Szabó, Ágnes; Váradi, Tímea; Kovács, Tamás; Batta, Gyula; Szöllősi, János

    2016-04-01

    Fluorescence or Förster resonance energy transfer (FRET) remains one of the most widely used methods for assessing protein clustering and conformation. Although it is a method with solid physical foundations, many applications of FRET fall short of providing quantitative results due to inappropriate calibration and controls. This shortcoming is especially valid for microscopy where currently available tools have limited or no capability at all to display parameter distributions or to perform gating. Since users of multiparameter flow cytometry usually apply these tools, the absence of these features in applications developed for microscopic FRET analysis is a significant limitation. Therefore, we developed a graphical user interface-controlled Matlab application for the evaluation of ratiometric, intensity-based microscopic FRET measurements. The program can calculate all the necessary overspill and spectroscopic correction factors and the FRET efficiency and it displays the results on histograms and dot plots. Gating on plots and mask images can be used to limit the calculation to certain parts of the image. It is an important feature of the program that the calculated parameters can be determined by regression methods, maximum likelihood estimation (MLE) and from summed intensities in addition to pixel-by-pixel evaluation. The confidence interval of calculated parameters can be estimated using parameter simulations if the approximate average number of detected photons is known. The program is not only user-friendly, but it provides rich output, it gives the user freedom to choose from different calculation modes and it gives insight into the reliability and distribution of the calculated parameters. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.

  13. A communication theoretical analysis of FRET-based mobile ad hoc molecular nanonetworks.

    Science.gov (United States)

    Kuscu, Murat; Akan, Ozgur B

    2014-09-01

    Nanonetworks refer to a group of nanosized machines with very basic operational capabilities communicating to each other in order to accomplish more complex tasks such as in-body drug delivery, or chemical defense. Realizing reliable and high-rate communication between these nanomachines is a fundamental problem for the practicality of these nanonetworks. Recently, we have proposed a molecular communication method based on Förster Resonance Energy Transfer (FRET) which is a nonradiative excited state energy transfer phenomenon observed among fluorescent molecules, i.e., fluorophores. We have modeled the FRET-based communication channel considering the fluorophores as single-molecular immobile nanomachines, and shown its reliability at high rates, and practicality at the current stage of nanotechnology. In this study, for the first time in the literature, we investigate the network of mobile nanomachines communicating through FRET. We introduce two novel mobile molecular nanonetworks: FRET-based mobile molecular sensor/actor nanonetwork (FRET-MSAN) which is a distributed system of mobile fluorophores acting as sensor or actor node; and FRET-based mobile ad hoc molecular nanonetwork (FRET-MAMNET) which consists of fluorophore-based nanotransmitter, nanoreceivers and nanorelays. We model the single message propagation based on birth-death processes with continuous time Markov chains. We evaluate the performance of FRET-MSAN and FRET-MAMNET in terms of successful transmission probability and mean extinction time of the messages, system throughput, channel capacity and achievable communication rates.

  14. Intercalating dye as an acceptor in quantum-dot-mediated FRET

    International Nuclear Information System (INIS)

    Lim, Teck Chuan; Bailey, Vasudev J; Wang, T-H; Ho, Y-P

    2008-01-01

    Fluorescence resonance energy transfer (FRET) is a popular tool to study intermolecular distances and characterize structural or conformational changes of biological macromolecules. We investigate a novel inorganic/organic FRET pair with quantum dots (QDs) as donors and DNA intercalating dyes, BOBO-3, as acceptors by using DNA as a linker. Typically, FRET efficiency increases with the number of stained DNA linked to a QD. However, with the use of intercalating dyes, we demonstrate that FRET efficiency at a fixed DNA:QD ratio can be further enhanced by increasing the number of dyes stained to a DNA strand through the use of an increased staining dye/bp ratio. We exploit this flexibility in the staining ratio to maintain a high FRET efficiency of >0.90 despite a sixfold decrease in DNA concentration. Having characterized this new QD-mediated FRET system, we test this system in a cellular environment using nanocomplexes generated by encapsulating DNA with commercial non-viral gene carriers. Using this novel FRET pair, we are able to monitor the configuration changes and fate of the DNA nanocomplexes during intracellular delivery, thereby providing an insight into the mechanistic study of gene delivery

  15. Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting

    OpenAIRE

    Bajar, Bryce T.; Wang, Emily S.; Lam, Amy J.; Kim, Bongjae B.; Jacobs, Conor L.; Howe, Elizabeth S.; Davidson, Michael W.; Lin, Michael Z.; Chu, Jun

    2016-01-01

    Many genetically encoded biosensors use F?rster resonance energy transfer (FRET) to dynamically report biomolecular activities. While pairs of cyan and yellow fluorescent proteins (FPs) are most commonly used as FRET partner fluorophores, respectively, green and red FPs offer distinct advantages for FRET, such as greater spectral separation, less phototoxicity, and lower autofluorescence. We previously developed the green-red FRET pair Clover and mRuby2, which improves responsiveness in intra...

  16. A fluorescence resonance energy transfer (FRET) biosensor based on graphene quantum dots (GQDs) and gold nanoparticles (AuNPs) for the detection of mecA gene sequence of Staphylococcus aureus.

    Science.gov (United States)

    Shi, Jingyu; Chan, Chunyu; Pang, Yukting; Ye, Weiwei; Tian, Feng; Lyu, Jing; Zhang, Yu; Yang, Mo

    2015-05-15

    In this work, a novel fluorescence resonance energy transfer (FRET) biosensor based on graphene quantum dots (GQDs) and gold nanoparticles (AuNPs) pairs was developed for Staphylococcus aureus specific gene sequence detection. This FRET biosensor platform was realized by immobilization of capture probes on GQDs and conjugation of reporter probes on AuNPs. Target oligos then co-hybridized with capture probes and reporter probes to form a sandwich structure which brought GQDs and AuNPs to close proximity to trigger FRET effect. The fluorescence signals before and after addition of targets were measured and the fluorescence quenching efficiency could reach around 87% with 100 nM target oligo. The limit of detection (LOD) of this FRET biosensor was around 1 nM for S.aureus gene detection. Experiments with both single-base mismatched oligos and double-base mismatched oligos demonstrated the good sequence selectivity of this FRET biosensor. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Roughness Effects on Fretting Fatigue

    Science.gov (United States)

    Yue, Tongyan; Abdel Wahab, Magd

    2017-05-01

    Fretting is a small oscillatory relative motion between two normal loaded contact surfaces. It may cause fretting fatigue, fretting wear and/or fretting corrosion damage depending on various fretting couples and working conditions. Fretting fatigue usually occurs at partial slip condition, and results in catastrophic failure at the stress levels below the fatigue limit of the material. Many parameters may affect fretting behaviour, including the applied normal load and displacement, material properties, roughness of the contact surfaces, frequency, etc. Since fretting damage is undesirable due to contacting, the effect of rough contact surfaces on fretting damage has been studied by many researchers. Experimental method on this topic is usually focusing on rough surface effects by finishing treatment and random rough surface effects in order to increase fretting fatigue life. However, most of numerical models on roughness are based on random surface. This paper reviewed both experimental and numerical methodology on the rough surface effects on fretting fatigue.

  18. Developing Fast Fluorescent Protein Voltage Sensors by Optimizing FRET Interactions.

    Directory of Open Access Journals (Sweden)

    Uhna Sung

    Full Text Available FRET (Förster Resonance Energy Transfer-based protein voltage sensors can be useful for monitoring neuronal activity in vivo because the ratio of signals between the donor and acceptor pair reduces common sources of noise such as heart beat artifacts. We improved the performance of FRET based genetically encoded Fluorescent Protein (FP voltage sensors by optimizing the location of donor and acceptor FPs flanking the voltage sensitive domain of the Ciona intestinalis voltage sensitive phosphatase. First, we created 39 different "Nabi1" constructs by positioning the donor FP, UKG, at 8 different locations downstream of the voltage-sensing domain and the acceptor FP, mKO, at 6 positions upstream. Several of these combinations resulted in large voltage dependent signals and relatively fast kinetics. Nabi1 probes responded with signal size up to 11% ΔF/F for a 100 mV depolarization and fast response time constants both for signal activation (~2 ms and signal decay (~3 ms. We improved expression in neuronal cells by replacing the mKO and UKG FRET pair with Clover (donor FP and mRuby2 (acceptor FP to create Nabi2 probes. Nabi2 probes also had large signals and relatively fast time constants in HEK293 cells. In primary neuronal culture, a Nabi2 probe was able to differentiate individual action potentials at 45 Hz.

  19. Fluorescent protein pair emit intracellular FRET signal suitable for FACS screening

    International Nuclear Information System (INIS)

    Johansson, Daniel X.; Brismar, Hjalmar; Persson, Mats A.A.

    2007-01-01

    The fluorescent proteins ECFP and HcRed were shown to give an easily resolved FRET-signal when expressed as a fusion inside mammalian cells. HeLa-tat cells expressing ECFP, pHcRed, or the fusion protein pHcRed-ECFP were analyzed by flow cytometry after excitation of ECFP. Cells expressing HcRed-ECFP, or ECFP and HcRed, were mixed and FACS-sorted for FRET positive cells: HcRed-ECFP cells were greatly enriched (72 times). Next, cloned human antibodies were fused with ECFP and expressed anchored to the ER membrane. Their cognate antigens (HIV-1 gp120 or gp41) were fused to HcRed and co-expressed in the ER. An increase of 13.5 ± 1.5% (mean ± SEM) and 8.0 ± 0.7% in ECFP fluorescence for the specific antibodies reacting with gp120 or gp41, respectively, was noted after photobleaching. A positive control (HcRed-ECFP) gave a 14.8 ± 2.6% increase. Surprisingly, the unspecific antibody (anti-TT) showed 12.1 ± 1.1% increase, possibly because overexpression in the limited ER compartment gave false FRET signals

  20. Reconstruction of calmodulin single-molecule FRET states, dye interactions, and CaMKII peptide binding by MultiNest and classic maximum entropy

    Science.gov (United States)

    DeVore, Matthew S.; Gull, Stephen F.; Johnson, Carey K.

    2013-08-01

    We analyzed single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.

  1. Reconstruction of Calmodulin Single-Molecule FRET States, Dye-Interactions, and CaMKII Peptide Binding by MultiNest and Classic Maximum Entropy.

    Science.gov (United States)

    Devore, Matthew S; Gull, Stephen F; Johnson, Carey K

    2013-08-30

    We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca 2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.

  2. FRET-mediated pH-responsive dual fluorescent nanoparticles prepared via click chemistry

    Science.gov (United States)

    Ouadahi, Karima; Sbargoud, Kamal; Allard, Emmanuel; Larpent, Chantal

    2012-01-01

    Herein, we report an easy preparation of azide-coated polystyrene-based nanoparticles (15 nm in diameter) and their surface functionalization via CuAAC with fluorophores in water. Resultant dual fluorescent nanoparticles coated with dansyl and pH-sensitive fluorescein moieties as the donor/acceptor FRET pair show a ratiometric response to pH upon excitation at a single wavelength.Herein, we report an easy preparation of azide-coated polystyrene-based nanoparticles (15 nm in diameter) and their surface functionalization via CuAAC with fluorophores in water. Resultant dual fluorescent nanoparticles coated with dansyl and pH-sensitive fluorescein moieties as the donor/acceptor FRET pair show a ratiometric response to pH upon excitation at a single wavelength. Electronic supplementary information (ESI) available: Experimental details and figures S1-S16 as mentioned in the text. See DOI: 10.1039/c2nr11413e

  3. A FRET-based probe for epidermal growth factor receptor bound non-covalently to a pair of synthetic amphipathic helixes

    International Nuclear Information System (INIS)

    Itoh, Reina E.; Kurokawa, Kazuo; Fujioka, Aki; Sharma, Alok; Mayer, Bruce J.; Matsuda, Michiyuki

    2005-01-01

    Epidermal growth factor (EGF) receptor plays a pivotal role in a variety of cellular functions, such as proliferation, differentiation, and migration. To monitor the EGF receptor (EGFR) activity in living cells, we developed a probe for EGFR activity based on the principle of fluorescence resonance energy transfer (FRET). Previously, we developed a probe designated as Picchu (Phosphorylation indicator of the CrkII chimeric unit), which detects the tyrosine phosphorylation of the CrkII adaptor protein. We used a pair of synthetic amphipathic helixes, WinZipA2 and WinZipB1, to bind Picchu non-covalently to the carboxyl-terminus of the EGFR. Using this modified probe named Picchu-Z, the activity of EGFR was followed in EGF-stimulated Cos7 cells. We found that a high level of tyrosine phosphorylation of Picchu-Z probe remained after endocytosis until the point when the EGFR was translocated to the perinuclear region. These findings are in agreement with the previously reported 'signaling endosome' model. Furthermore, by pulse stimulation with EGF and by acute ablation of EGFR activity with AG1478, it was suggested that the phosphorylation of Picchu-Z probe, and probably the phosphorylation of EGFR also, underwent a rapid equilibrium (τ 1/2 < 2 min) between the phosphorylated and dephosphorylated states in the presence of EGF

  4. QD-Based FRET Probes at a Glance

    Directory of Open Access Journals (Sweden)

    Armen Shamirian

    2015-06-01

    Full Text Available The unique optoelectronic properties of quantum dots (QDs give them significant advantages over traditional organic dyes, not only as fluorescent labels for bioimaging, but also as emissive sensing probes. QD sensors that function via manipulation of fluorescent resonance energy transfer (FRET are of special interest due to the multiple response mechanisms that may be utilized, which in turn imparts enhanced flexibility in their design. They may also function as ratiometric, or “color-changing” probes. In this review, we describe the fundamentals of FRET and provide examples of QD-FRET sensors as grouped by their response mechanisms such as link cleavage and structural rearrangement. An overview of early works, recent advances, and various models of QD-FRET sensors for the measurement of pH and oxygen, as well as the presence of metal ions and proteins such as enzymes, are also provided.

  5. N-way FRET microscopy of multiple protein-protein interactions in live cells.

    Directory of Open Access Journals (Sweden)

    Adam D Hoppe

    Full Text Available Fluorescence Resonance Energy Transfer (FRET microscopy has emerged as a powerful tool to visualize nanoscale protein-protein interactions while capturing their microscale organization and millisecond dynamics. Recently, FRET microscopy was extended to imaging of multiple donor-acceptor pairs, thereby enabling visualization of multiple biochemical events within a single living cell. These methods require numerous equations that must be defined on a case-by-case basis. Here, we present a universal multispectral microscopy method (N-Way FRET to enable quantitative imaging for any number of interacting and non-interacting FRET pairs. This approach redefines linear unmixing to incorporate the excitation and emission couplings created by FRET, which cannot be accounted for in conventional linear unmixing. Experiments on a three-fluorophore system using blue, yellow and red fluorescent proteins validate the method in living cells. In addition, we propose a simple linear algebra scheme for error propagation from input data to estimate the uncertainty in the computed FRET images. We demonstrate the strength of this approach by monitoring the oligomerization of three FP-tagged HIV Gag proteins whose tight association in the viral capsid is readily observed. Replacement of one FP-Gag molecule with a lipid raft-targeted FP allowed direct observation of Gag oligomerization with no association between FP-Gag and raft-targeted FP. The N-Way FRET method provides a new toolbox for capturing multiple molecular processes with high spatial and temporal resolution in living cells.

  6. Molecularly imprinted fluorescent probe based on FRET for selective and sensitive detection of doxorubicin

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhifeng, E-mail: 897061147@qq.com [College of Chemistry and Materials Science, Hengyang Normal University, Key Laboratory of Functional Organometallic Materials of Hunan Province University, Hengyang 421008 (China); Deng, Peihong; Li, Junhua [College of Chemistry and Materials Science, Hengyang Normal University, Key Laboratory of Functional Organometallic Materials of Hunan Province University, Hengyang 421008 (China); Xu, Li [Department of Applied Chemistry, College of Materials and Energy, South China Agricultural University, Guangzhou 510642 (China); Tang, Siping [College of Chemistry and Materials Science, Hengyang Normal University, Key Laboratory of Functional Organometallic Materials of Hunan Province University, Hengyang 421008 (China)

    2017-04-15

    Highlights: • FRET-based molecularly imprinted probe for detection of doxorubicin was prepared. • The detection limit of the probe was 13.8 nM for doxorubicin. • The FRET-based probe had a higher selectivity for the template than ordinary MIMs. - Abstract: In this work, a new type of fluorescent probe for detection of doxorubicin has been constructed by the combined use of fluorescence resonance energy transfer (FRET) technology and molecular imprinting technique (MIT). Using doxorubicin as the template, the molecularly imprinted polymer thin layer was fabricated on the surfaces of carbon dot (CD) modified silica by sol-gel polymerization. The excitation energy of the fluorescent donor (CDs) could be transferred to the fluorescent acceptor (doxorubicin). The FRET based fluorescent probe demonstrated high sensitivity and selectivity for doxorubicin. The detection limit was 13.8 nM. The fluorescent probe was successfully applied for detecting doxorubicin in doxorubicin-spiked plasmas with a recovery of 96.8–103.8%, a relative standard deviation (RSD) of 1.3–2.8%. The strategy for construction of FRET-based molecularly imprinted materials developed in this work is very promising for analytical applications.

  7. Multi step FRET among three laser dyes Pyrene, Acriflavine and Rhodamine B

    International Nuclear Information System (INIS)

    Saha, Jaba; Dey, Dibyendu; Roy, Arpan Datta; Bhattacharjee, D.; Hussain, Syed Arshad

    2016-01-01

    Fluorescence Resonance Energy Transfer (FRET) system using three dyes has been demonstrated. It has been observed that multi step energy transfer occurred from Pyrene to Rhodamine B via Acriflavine. Here Acriflavine acts as an antenna to receive energy from Pyrene and transfer the same to Rhodamine B. This multi step FRET system is advantageous compared to the conventional FRET as this can be used to study molecular level interaction beyond conventional FRET distance (1–10 nm) as well as studying multi-branched macromolecules. The introduction of clay enhances the FRET efficiencies among the dye pair, which is an advantage to make the multi step system more useful. Similar approach can be used for increasing FRET efficiencies by using other dyes. - Highlights: • Multi-step FRET occurred from Pyrene (Py) to Rhodamine B (RhB) via Acriflavine (Acf). • Acf acts as an antenna to receive energy from Py and to transfer energy to RhB. • Multi-step FRET can be used to study molecular level interaction beyond 1–10 nm. • Incorporation of nanoclay laponite enhances the energy transfer efficiency.

  8. Partially reduced graphene oxide based FRET on fiber-optic interferometer for biochemical detection.

    Science.gov (United States)

    Yao, B C; Wu, Y; Yu, C B; He, J R; Rao, Y J; Gong, Y; Fu, F; Chen, Y F; Li, Y R

    2016-03-24

    Fluorescent resonance energy transfer (FRET) with naturally exceptional selectivity is a powerful technique and widely used in chemical and biomedical analysis. However, it is still challenging for conventional FRET to perform as a high sensitivity compact sensor. Here we propose a novel 'FRET on Fiber' concept, in which a partially reduced graphene oxide (prGO) film is deposited on a fiber-optic modal interferometer, acting as both the fluorescent quencher for the FRET and the sensitive cladding for optical phase measurement due to refractive index changes in biochemical detection. The target analytes induced fluorescence recovery with good selectivity and optical phase shift with high sensitivity are measured simultaneously. The functionalized prGO film coated on the fiber-optic interferometer shows high sensitivities for the detections of metal ion, dopamine and single-stranded DNA (ssDNA), with detection limits of 1.2 nM, 1.3 μM and 1 pM, respectively. Such a prGO based 'FRET on fiber' configuration, bridging the FRET and the fiber-optic sensing technology, may serve as a platform for the realization of series of integrated 'FRET on Fiber' sensors for on-line environmental, chemical, and biomedical detection, with excellent compactness, high sensitivity, good selectivity and fast response.

  9. Highly sensitive and quantitative FRET-FLIM imaging in single dendritic spines using improved non-radiative YFP.

    Science.gov (United States)

    Murakoshi, Hideji; Lee, Seok-Jin; Yasuda, Ryohei

    2008-08-01

    Two-photon fluorescence lifetime imaging microscopy (TPFLIM) enables the quantitative measurements of fluorescence resonance energy transfer (FRET) in small subcellular compartments in light scattering tissue. We evaluated and optimized the FRET pair of mEGFP (monomeric EGFP with the A206K mutation) and REACh (non-radiative YFP variants) for TPFLIM. We characterized several mutants of REACh in terms of their "darkness," and their ability to act as a FRET acceptor for mEGFP in HeLa cells and hippocampal neurons. Since the commonly used monomeric mutation A206K increases the brightness of REACh, we introduced a different monomeric mutation (F223R) which does not affect the brightness. Also, we found that the folding efficiency of original REACh, as measured by the fluorescence lifetime of a mEGFP-REACh tandem dimer, was low and variable from cell to cell. Introducing two folding mutations (F46L, Q69M) into REACh increased the folding efficiency by approximately 50%, and reduced the variability of FRET signal. Pairing mEGFP with the new REACh (super-REACh, or sREACh) improved the signal-to-noise ratio compared to the mEGFP-mRFP or mEGFP-original REACh pair by approximately 50%. Using this new pair, we demonstrated that the fraction of actin monomers in filamentous and globular forms in single dendritic spines can be quantitatively measured with high sensitivity. Thus, the mEGFP-sREACh pair is suited for quantitative FRET measurement by TPFLIM, and enables us to measure protein-protein interactions in individual dendritic spines in brain slices with high sensitivity.

  10. Detecting analogical resemblance without retrieving the source analogy.

    Science.gov (United States)

    Kostic, Bogdan; Cleary, Anne M; Severin, Kaye; Miller, Samuel W

    2010-06-01

    We examined whether people can detect analogical resemblance to an earlier experimental episode without being able to recall the experimental source of the analogical resemblance. We used four-word analogies (e.g., robin-nest/beaver-dam), in a variation of the recognition-without-cued-recall method (Cleary, 2004). Participants studied word pairs (e.g., robin-nest) and were shown new word pairs at test, half of which analogically related to studied word pairs (e.g., beaver-dam) and half of which did not. For each test pair, participants first attempted to recall an analogically similar pair from the study list. Then, regardless of whether successful recall occurred, participants were prompted to rate the familiarity of the test pair, which was said to indicate the likelihood that a pair that was analogically similar to the test pair had been studied. Across three experiments, participants demonstrated an ability to detect analogical resemblance without recalling the source analogy. Findings are discussed in terms of their potential relevance to the study of analogical reasoning and insight, as well as to the study of familiarity and recognition memory.

  11. Lateral distribution of NBD-PC fluorescent lipid analogs in membranes probed by molecular dynamics-assisted analysis of Förster Resonance Energy Transfer (FRET) and fluorescence quenching.

    Science.gov (United States)

    Loura, Luís M S

    2012-11-08

    Förster resonance energy transfer (FRET) is a powerful tool used for many problems in membrane biophysics, including characterization of the lateral distribution of lipid components and other species of interest. However, quantitative analysis of FRET data with a topological model requires adequate choices for the values of several input parameters, some of which are difficult to obtain experimentally in an independent manner. For this purpose, atomistic molecular dynamics (MD) simulations can be potentially useful as they provide direct detailed information on transverse probe localization, relative probe orientation, and membrane surface area, all of which are required for analysis of FRET data. This is illustrated here for the FRET pairs involving 1,6-diphenylhexatriene (DPH) as donor and either 1-palmitoyl,2-(6-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino] hexanoyl)- sn-glycero-3-phosphocholine (C6-NBD-PC) or 1-palmitoyl,2-(12-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]dodecanoyl)-sn-glycero-3-phosphocholine (C12-NBD-PC) as acceptors, in fluid vesicles of 1,2-dipalmitoyl-sn-3-glycerophosphocholine (DPPC, 50 °C). Incorporation of results from MD simulations improves the statistical quality of model fitting to the experimental FRET data. Furthermore, the decay of DPH in the presence of moderate amounts of C12-NBD-PC (>0.4 mol%) is consistent with non-random lateral distribution of the latter, at variance with C6-NBD-PC, for which aggregation is ruled out up to 2.5 mol% concentration. These conclusions are supported by analysis of NBD-PC fluorescence self-quenching. Implications regarding the relative utility of these probes in membrane studies are discussed.

  12. Dual door entry to exciplex emission in a chimeric DNA duplex containing non-nucleoside-nucleoside pair.

    Science.gov (United States)

    Bag, Subhendu Sekhar; Talukdar, Sangita; Kundu, Rajen; Saito, Isao; Jana, Subhashis

    2014-01-25

    Dual door entry to exciplex formation was established in a chimeric DNA duplex wherein a fluorescent non-nucleosidic base surrogate () is paired against a fluorescent nucleosidic base surrogate (). Packing of the nucleobases via intercalative stacking interactions led to an exciplex emission either via FRET from the donor or direct excitation of the FRET acceptor .

  13. Ultrasensitive FRET-based DNA sensor using PNA/DNA hybridization.

    Science.gov (United States)

    Yang, Lan-Hee; Ahn, Dong June; Koo, Eunhae

    2016-12-01

    In the diagnosis of genetic diseases, rapid and highly sensitive DNA detection is crucial. Therefore, many strategies for detecting target DNA have been developed, including electrical, optical, and mechanical methods. Herein, a highly sensitive FRET based sensor was developed by using PNA (Peptide Nucleic Acid) probe and QD, in which red color QDs are hybridized with capture probes, reporter probes and target DNAs by EDC-NHS coupling. The hybridized probe with target DNA gives off fluorescent signal due to the energy transfer from QD to Cy5 dye in the reporter probe. Compared to the conventional DNA sensor using DNA probes, the DNA sensor using PNA probes shows higher FRET factor and efficiency due to the higher reactivity between PNA and target DNA. In addition, to elicit the effect of the distance between the donor and the acceptor, we have investigated two types of the reporter probes having Cy5 dyes attached at the different positions of the reporter probes. Results show that the shorter the distance between QDs and Cy5s, the stronger the signal intensity. Furthermore, based on the fluorescence microscopy images using microcapillary chips, the FRET signal is enhanced to be up to 276% times stronger than the signal obtained using the cuvette by the fluorescence spectrometer. These results suggest that the PNA probe system conjugated with QDs can be used as ultrasensitive DNA nanosensors. Copyright © 2016. Published by Elsevier B.V.

  14. Simultaneous live cell imaging using dual FRET sensors with a single excitation light.

    Directory of Open Access Journals (Sweden)

    Yusuke Niino

    Full Text Available Fluorescence resonance energy transfer (FRET between fluorescent proteins is a powerful tool for visualization of signal transduction in living cells, and recently, some strategies for imaging of dual FRET pairs in a single cell have been reported. However, these necessitate alteration of excitation light between two different wavelengths to avoid the spectral overlap, resulting in sequential detection with a lag time. Thus, to follow fast signal dynamics or signal changes in highly motile cells, a single-excitation dual-FRET method should be required. Here we reported this by using four-color imaging with a single excitation light and subsequent linear unmixing to distinguish fluorescent proteins. We constructed new FRET sensors with Sapphire/RFP to combine with CFP/YFP, and accomplished simultaneous imaging of cAMP and cGMP in single cells. We confirmed that signal amplitude of our dual FRET measurement is comparable to of conventional single FRET measurement. Finally, we demonstrated to monitor both intracellular Ca(2+ and cAMP in highly motile cardiac myocytes. To cancel out artifacts caused by the movement of the cell, this method expands the applicability of the combined use of dual FRET sensors for cell samples with high motility.

  15. Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting.

    Science.gov (United States)

    Bajar, Bryce T; Wang, Emily S; Lam, Amy J; Kim, Bongjae B; Jacobs, Conor L; Howe, Elizabeth S; Davidson, Michael W; Lin, Michael Z; Chu, Jun

    2016-02-16

    Many genetically encoded biosensors use Förster resonance energy transfer (FRET) to dynamically report biomolecular activities. While pairs of cyan and yellow fluorescent proteins (FPs) are most commonly used as FRET partner fluorophores, respectively, green and red FPs offer distinct advantages for FRET, such as greater spectral separation, less phototoxicity, and lower autofluorescence. We previously developed the green-red FRET pair Clover and mRuby2, which improves responsiveness in intramolecular FRET reporters with different designs. Here we report the engineering of brighter and more photostable variants, mClover3 and mRuby3. mClover3 improves photostability by 60% and mRuby3 by 200% over the previous generation of fluorophores. Notably, mRuby3 is also 35% brighter than mRuby2, making it both the brightest and most photostable monomeric red FP yet characterized. Furthermore, we developed a standardized methodology for assessing FP performance in mammalian cells as stand-alone markers and as FRET partners. We found that mClover3 or mRuby3 expression in mammalian cells provides the highest fluorescence signals of all jellyfish GFP or coral RFP derivatives, respectively. Finally, using mClover3 and mRuby3, we engineered an improved version of the CaMKIIα reporter Camuiα with a larger response amplitude.

  16. Wide-field lifetime-based FRET imaging for the assessment of early functional distribution of transferrin-based delivery in breast tumor-bearing small animals

    Science.gov (United States)

    Sinsuebphon, Nattawut; Rudkouskaya, Alena; Barroso, Margarida; Intes, Xavier

    2016-02-01

    Targeted drug delivery is a critical aspect of successful cancer therapy. Assessment of dynamic distribution of the drug provides relative concentration and bioavailability at the target tissue. The most common approach of the assessment is intensity-based imaging, which only provides information about anatomical distribution. Observation of biomolecular interactions can be performed using Förster resonance energy transfer (FRET). Thus, FRET-based imaging can assess functional distribution and provide potential therapeutic outcomes. In this study, we used wide-field lifetime-based FRET imaging for the study of early functional distribution of transferrin delivery in breast cancer tumor models in small animals. Transferrin is a carrier for cancer drug delivery. Its interaction with its receptor is within a few nanometers, which is suitable for FRET. Alexa Fluor® 700 and Alexa Fluor® 750 were conjugated to holo-transferrin which were then administered via tail vein injection to the mice implanted with T47D breast cancer xenografts. Images were continuously acquired for 60 minutes post-injection. The results showed that transferrin was primarily distributed to the liver, the urinary bladder, and the tumor. The cellular uptake of transferrin, which was indicated by the level of FRET, was high in the liver but very low in the urinary bladder. The results also suggested that the fluorescence intensity and FRET signals were independent. The liver showed increasing intensity and increasing FRET during the observation period, while the urinary bladder showed increasing intensity but minimal FRET. Tumors gave varied results corresponding to their FRET progression. These results were relevant to the biomolecular events that occurred in the animals.

  17. Stuy on Fatigue Life of Aluminum Alloy Considering Fretting

    Science.gov (United States)

    Yang, Maosheng; Zhao, Hongqiang; Wang, Yunxiang; Chen, Xiaofei; Fan, Jiali

    2018-01-01

    To study the influence of fretting on Aluminum Alloy, a global finite element model considering fretting was performed using the commercial code ABAQUS. With which a new model for predicting fretting fatigue life has been presented based on friction work. The rationality and effectiveness of the model were validated according to the contrast of experiment life and predicting life. At last influence factor on fretting fatigue life of aerial aluminum alloy was investigated with the model. The results revealed that fretting fatigue life decreased monotonously with the increasing of normal load and then became constant at higher pressures. At low normal load, fretting fatigue life was found to increase with increase in the pad radius. At high normal load, however, the fretting fatigue life remained almost unchanged with changes in the fretting pad radius. The bulk stress amplitude had the dominant effect on fretting fatigue life. The fretting fatigue life diminished as the bulk stress amplitude increased.

  18. Detection of protease activity by fluorescent protein FRET sensors: from computer simulation to live cells

    Science.gov (United States)

    Goryashchenko, Alexander S.; Khrenova, Maria G.; Savitsky, Alexander P.

    2018-04-01

    Förster resonance energy transfer (FRET) sensors are widely used for the detection of protease activity in vitro and in vivo. Usually they consist of a FRET pair connected with a polypeptide linker containing a specific cleavage site for the relevant protease. Use of the fluorescent proteins as components of the FRET pair allows genetic encoding of such sensors and solves the problem of their delivery into live cells and animals. There are several ways to improve the properties of such sensors, mainly to increase FRET efficiency and therefore the dynamic range. One of the ways to achieve this is to use a non-fluorescent chromoprotein as an acceptor. Molecular dynamic simulations may assist in the construction of linker structures connecting donor and acceptor molecules. Estimation of the orientation factor κ 2 can be obtained by methods based on quantum theory and combined quantum mechanics/molecular mechanics approaches. The linker can be structured by hydrophobic interactions, bringing it into a closed conformation that shortens the distance between donor and acceptor and, consequently, increases FRET efficiency. We analyzed the effects of different linker structures on the detection of caspase-3 activity using a non-fluorescent acceptor. Also we have constructed the Tb3+- TagRFP sensor in which a complex of the terbium ion and terbium-binding peptide is used as a donor. This allowed us to use the unique property of lanthanide ions—fluorescence lifetime up to milliseconds—to perform measurements with time delay and exclude the nanosecond-order fluorescence. Using our systems as a starting point, by changing the recognition site in the linker it is possible to perform imaging of different protease activity in vitro or in vivo.

  19. Studying DNA looping by single-molecule FRET.

    Science.gov (United States)

    Le, Tung T; Kim, Harold D

    2014-06-28

    Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.

  20. A new trend to determine biochemical parameters by quantitative FRET assays.

    Science.gov (United States)

    Liao, Jia-yu; Song, Yang; Liu, Yan

    2015-12-01

    Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research because it can determine molecule or particle interactions within a range of 1-10 nm. The sensitivity and efficiency of FRET strongly depend on the distance between the FRET donor and acceptor. Historically, FRET assays have been used to quantitatively deduce molecular distances. However, another major potential application of the FRET assay has not been fully exploited, that is, the use of FRET signals to quantitatively describe molecular interactive events. In this review, we discuss the use of quantitative FRET assays for the determination of biochemical parameters, such as the protein interaction dissociation constant (K(d)), enzymatic velocity (k(cat)) and K(m). We also describe fluorescent microscopy-based quantitative FRET assays for protein interaction affinity determination in cells as well as fluorimeter-based quantitative FRET assays for protein interaction and enzymatic parameter determination in solution.

  1. Fluorescence resonance energy transfer (FRET-based subcellular visualization of pathogen-induced host receptor signaling

    Directory of Open Access Journals (Sweden)

    Zimmermann Timo

    2009-11-01

    Full Text Available Abstract Background Bacteria-triggered signaling events in infected host cells are key elements in shaping the host response to pathogens. Within the eukaryotic cell, signaling complexes are spatially organized. However, the investigation of protein-protein interactions triggered by bacterial infection in the cellular context is technically challenging. Here, we provide a methodological approach to exploit fluorescence resonance energy transfer (FRET to visualize pathogen-initiated signaling events in human cells. Results Live-cell microscopy revealed the transient recruitment of the Src family tyrosine kinase Hck upon bacterial engagement of the receptor carcinoembryonic antigen-related cell adhesion molecule 3 (CEACAM3. In cells expressing a CEACAM3 variant lacking the cytoplasmic domain, the Src homology 2 (SH2 domain of Hck (Hck-SH2 was not recruited, even though bacteria still bound to the receptor. FRET measurements on the basis of whole cell lysates revealed intimate binding between Hck-SH2 (using enhanced yellow fluorescent protein (YPet-Hck-SH2 and the tyrosine-phosphorylated enhanced cyan fluorescent protein-labeled cytoplasmic domain of wild-type CEACAM3 (CEACAM3 WT-CyPet and a flow cytometry-based FRET approach verified this association in intact cells. Using confocal microscopy and acceptor photobleaching, FRET between Hck-SH2 and CEACAM3 was localized to the sites of bacteria-host cell contact. Conclusion These data demonstrate not only the intimate binding of the SH2 domain of Hck to the tyrosine-phosphorylated cytoplasmic domain of CEACAM3 in intact cells, but furthermore, FRET measurements allow the subcellular localization of this process during bacterial infection. FRET-based assays are valuable tools to resolve bacteria-induced protein-protein interactions in the context of the intact host cell.

  2. NIR FRET Fluorophores for Use as an Implantable Glucose Biosensor

    Directory of Open Access Journals (Sweden)

    Majed DWEIK

    2008-12-01

    Full Text Available Development of an in vivo optical sensor requires the utilization of Near Infra Red (NIR fluorophores due to their ability to operate within the biological tissue window. Alexa Fluor 750 (AF750 and Alexa Fluor 680 (AF680 were examined as potential NIR fluorophores for an in vivo fluorescence resonance energy transfer (FRET glucose biosensor. AF680 and AF750 found to be a FRET pair and percent energy transfer was calculated. Next, the tested dye pair was utilized in a competitive binding assay in order to detect glucose. Concanavalin A (Con A and dextran have binding affinity, but in the presence of glucose, glucose displaces dextran due to its higher affinity to Con A than dextran. Finally, the percent signal transfer through porcine skin was examined. The results showed with approximately 4.0 mm porcine skin thickness, 1.98 % of the fluorescence was transmitted and captured by the detector.

  3. Graphene and graphene-like two-denominational materials based fluorescence resonance energy transfer (FRET) assays for biological applications.

    Science.gov (United States)

    Tian, Feng; Lyu, Jing; Shi, Jingyu; Yang, Mo

    2017-03-15

    In the past decades, Förster resonance energy transfer (FRET) has been applied in many biological applications to reveal the biological information at the nanoscale. Recently, graphene and graphene-like two-dimensional (2D) nanomaterials started to be used in FRET assays as donors or acceptors including graphene oxide (GO), graphene quantum dot (GQD), graphitic-carbon nitride nanosheets (g-C 3 N 4 ) and transition metal dichalcogenides (e.g. MoS 2 , MnO 2, and WS 2 ). Due to the remarkable properties such as large surface to volume ratio, tunable energy band, photoluminescence and excellent biocompatibility, these 2D nanomaterials based FRET assays have shown great potential in various biological applications. This review summarizes the recent development of graphene and graphene-like 2D nanomaterials based FRET assays in applications of biosensing, bioimaging, and drug delivery monitoring. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Prediction of fretting fatigue behavior under elastic-plastic conditions

    International Nuclear Information System (INIS)

    Shin, Ki Su

    2009-01-01

    Fretting fatigue generally leads to the degradation of the fatigue strength of a material due to cyclic micro-slip between two contacting materials. Fretting fatigue is regarded as an important issue in designing aerospace structures. While many studies have evaluated fretting fatigue behavior under elastic deformation conditions, few have focused on fretting fatigue behavior under elastic-plastic deformation conditions, especially the crack orientation and fatigue life prediction for Ti-6Al-4V. The primary goal of this study was to characterize the fretting fatigue crack initiation behavior in the presence of plasticity. Experimental tests were performed using pad configurations involving elastic-plastic deformations. To calculate stress distributions under elastic-plastic fretting fatigue conditions, FEA was also performed. Several parametric approaches were used to predict fretting fatigue life along with stress distribution resulting from FEA. However, those parameters using surface stresses were unable to establish an equivalence between elastic fretting fatigue data and elastic-plastic fretting fatigue data. Based on this observation, the critical distance methods, which are commonly used in notch analysis, were applied to the fretting fatigue problem. In conclusion, the effective strain range method when used in conjunction with the SMSSR parameter showed a good correlation of data points between the pad configurations involving elastic and elastic plastic deformations

  5. A Novel Water-soluble Ratiometric Fluorescent Probe Based on FRET for Sensing Lysosomal pH.

    Science.gov (United States)

    Song, Guang-Jie; Bai, Su-Yun; Luo, Jing; Cao, Xiao-Qun; Zhao, Bao-Xiang

    2016-11-01

    A new ratiometric fluorescent probe based on Förster resonance energy transfer (FRET) for sensing lysosomal pH has been developed. The probe (RMPM) was composed of imidazo[1,5-α]pyridine quaternary ammonium salt fluorophore as the FRET donor and the rhodamine moiety as the FRET acceptor. It's the first time to report that imidazo[1,5-α]pyridine quaternary ammonium salt acts as the FRET donor. The ratio of fluorescence intensity of the probe at two wavelengths (I 424 /I 581 ) changed significantly and responded linearly toward minor pH changes in the range of 5.4-6.6. It should be noted that it's rare to report that a ratiometric pH probe could detect so weak acidic pH with pKa = 6.31. In addition, probe RMPM exhibited excellent water-solubility, fast-response, all-right selectivity and brilliant reversibility. Moreover, RMPM has been successfully applied to sensing lysosomal pH in HeLa cells and has low cytotoxicity.

  6. A Toolbox of Genetically Encoded FRET-Based Biosensors for Rapid l-Lysine Analysis

    Directory of Open Access Journals (Sweden)

    Victoria Steffen

    2016-09-01

    Full Text Available Background: The fast development of microbial production strains for basic and fine chemicals is increasingly carried out in small scale cultivation systems to allow for higher throughput. Such parallelized systems create a need for new rapid online detection systems to quantify the respective target compound. In this regard, biosensors, especially genetically encoded Förster resonance energy transfer (FRET-based biosensors, offer tremendous opportunities. As a proof-of-concept, we have created a toolbox of FRET-based biosensors for the ratiometric determination of l-lysine in fermentation broth. Methods: The sensor toolbox was constructed based on a sensor that consists of an optimized central lysine-/arginine-/ornithine-binding protein (LAO-BP flanked by two fluorescent proteins (enhanced cyan fluorescent protein (ECFP, Citrine. Further sensor variants with altered affinity and sensitivity were obtained by circular permutation of the binding protein as well as the introduction of flexible and rigid linkers between the fluorescent proteins and the LAO-BP, respectively. Results: The sensor prototype was applied to monitor the extracellular l-lysine concentration of the l-lysine producing Corynebacterium glutamicum (C. glutamicum strain DM1933 in a BioLector® microscale cultivation device. The results matched well with data obtained by HPLC analysis and the Ninhydrin assay, demonstrating the high potential of FRET-based biosensors for high-throughput microbial bioprocess optimization.

  7. Ratiometric FRET-based detection of DNA and micro-RNA in solution

    International Nuclear Information System (INIS)

    Matveeva, Evgenia G.; Gryczynski, Zygmunt; Stewart, Donald R.; Gryczynski, Ignacy

    2009-01-01

    A ratiometric method for detecting DNA oligomers in bulk solution based on Foerster resonance energy transfer (FRET) is described. The two fluorescence signals (green and red), originating from Cy3 (donor, green) and Cy5 (acceptor, red) labels, are simultaneously detected from the pre-hybridized Cy3oligomerY:Cy5oligomerX system. The ratio of red to green intensities is sensitive to the presence of the single-stranded complimentary oligomer, which replaces single-stranded Cy3oligomerY in the donor:acceptor complex and perturbs the FRET. The detection scheme is generally applicable to the detection of DNA and RNA, and particularly micro-RNA. The proposed method is applicable to various double-stranded various lengths targets (manipulation of the sample preparation conditions, such as temperature, incubation time, denaturizing agent, may be needed).

  8. Standard guide for fretting fatigue testing

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2010-01-01

    1.1 This guide defines terminology and covers general requirements for conducting fretting fatigue tests and reporting the results. It describes the general types of fretting fatigue tests and provides some suggestions on developing and conducting fretting fatigue test programs. 1.2 Fretting fatigue tests are designed to determine the effects of mechanical and environmental parameters on the fretting fatigue behavior of metallic materials. This guide is not intended to establish preference of one apparatus or specimen design over others, but will establish guidelines for adherence in the design, calibration, and use of fretting fatigue apparatus and recommend the means to collect, record, and reporting of the data. 1.3 The number of cycles to form a fretting fatigue crack is dependent on both the material of the fatigue specimen and fretting pad, the geometry of contact between the two, and the method by which the loading and displacement are imposed. Similar to wear behavior of materials, it is important t...

  9. Decay time shortening of fluorescence from donor-acceptor pair proteins using ultrafast time-resolved fluorescence resonance energy transfer spectroscopy

    International Nuclear Information System (INIS)

    Baba, Motoyoshi; Suzuki, Masayuki; Ganeev, Rashid A.; Kuroda, Hiroto; Ozaki, Tsuneyuki; Hamakubo, Takao; Masuda, Kazuyuki; Hayashi, Masahiro; Sakihama, Toshiko; Kodama, Tatsuhiko; Kozasa, Tohru

    2007-01-01

    We improved an ultrafast time-resolved fluorescence resonance energy transfer (FRET) spectroscopy system and measured directly the decrease in the fluorescence decay time of the FRET signal, without any entanglement of components in the picosecond time scale from the donor-acceptor protein pairs (such as cameleon protein for calcium ion indicator, and ligand-activated GRIN-Go proteins pair). The drastic decrease in lifetime of the donor protein fluorescence under the FRET condition (e.g. a 47.8% decrease for a GRIN-Go protein pair) proves the deformation dynamics between donor and acceptor fluorescent proteins in an activated state of a mixed donor-acceptor protein pair. This study is the first clear evidence of physical contact of the GRIN-Go proteins pair using time-resolved FRET system. G protein-coupled receptors (GPCRs) are the most important protein family for the recognition of many chemical substances at the cell surface. They are the targets of many drugs. Simultaneously, we were able to observe the time-resolved spectra of luminous proteins at the initial stage under the FRET condition, within 10 ns from excitation. This new FRET system allows us to trace the dynamics of the interaction between proteins at the ligand-induced activated state, molecular structure change and combination or dissociation. It will be a key technology for the development of protein chip technology

  10. Rational design of FRET-based sensor proteins

    NARCIS (Netherlands)

    Merkx, M.

    2008-01-01

    Real-time imaging of molecular events inside living cells is important for understanding the basis of physiological processes and diseases. Genetically encoded sensors that use fluorescence resonance energy transfer (FRET) between two fluorescent proteins are attractive in this respect because they

  11. Sliding Wear and Fretting Wear of DLC-Based, Functionally Graded Nanocomposite Coatings

    Science.gov (United States)

    Miyoshi, K.; Pohlchuck, B.; Street, Kenneth W.; Zabinski, J. S.; Sanders, J. H.; Voevodin, A. a.; Wu, R. L. C.

    1999-01-01

    -DLC/Ti-Ti(sub x) C(sub y)-DLC-coated AISI 440C disk and on a titanium-6 wt % aluminum-4 wt% vanadium (Ti-6Al-4V) flat, both in contact with a 9.4-mm-diameter, hemispherical Ti-6Al-4V pin. The resistance to fretting wear and damage of the a-DLC/Ti-6Al-4V materials pair was superior to that of the Ti-6Al-4V/Ti-6AI-4V materials pair.

  12. A dansyl-rhodamine ratiometric fluorescent probe for Hg2+ based on FRET mechanism.

    Science.gov (United States)

    Xie, Puhui; Guo, Fengqi; Wang, Lingyu; Yang, Sen; Yao, Denghui; Yang, Guoyu

    2015-03-01

    Based on resonance energy transfer (FRET) from dansyl to rhodamine 101, a new fluorescent probe (compound 1) containing rhodamine 101 and a dansyl unit was synthesized for detecting Hg(2+) through ratiometric sensing in DMSO aqueous solutions. This probe shows a fast, reversible and selective response toward Hg(2+) in a wide pH range. Hg(2+) induced ring-opening reactions of the spirolactam rhodamine moiety of 1, leading to the formation of fluorescent derivatives that can serve as the FRET acceptors. Very large stokes shift (220 nm) was observed in this case. About 97-fold increase in fluorescence intensity ratio was observed upon its binding with Hg(2+).

  13. Understanding and modeling Förster-type resonance energy transfer (FRET) introduction to FRET

    CERN Document Server

    Govorov, Alexander; Demir, Hilmi Volkan

    2016-01-01

    This Brief presents a historical overview of the Förster-type nonradiative energy transfer and a compilation of important progress in FRET research, starting from Förster until today, along with a summary of the current state-of-the-art. Here the objective is to provide the reader with a complete account of important milestones in FRET studies and FRET applications as well as a picture of the current status.

  14. EXPERIMENTAL INVESTIGTION OF THE FRETTING PHENOMENON

    Directory of Open Access Journals (Sweden)

    Ştefan GHIMISI

    2015-12-01

    Full Text Available Fretting is now fully identified as a small amplitude oscilatory motion which induces a harmonic tangential force between two surfaces in contact.It is related to three main loadings, i.e. fretting-wear, fretting-fatigue and fretting corrosion.Fretting regimes were first mapped by Vingsbo. In a similar way, three fretting regimes will be considered: stick regime,slip regime and mixed regime. The mixed regime was made up of initial gross slip followed by partial slip condition after a few hundred cycles. Obviously the partial slip transition develops the highest stress levels which can induce fatigue crack nucleation depending on the fatigue properties of the two contacting first bodies. Therefore prediction of the frontier between partial slip and gross slip is required.

  15. The role of FRET in solar concentrator efficiency and color tunability

    Energy Technology Data Exchange (ETDEWEB)

    Balaban, Benjamin, E-mail: bbalaban@ucsc.edu; Doshay, Sage; Osborn, Melissa; Rodriguez, Yvonne; Carter, Sue A., E-mail: sacarter@ucsc.edu

    2014-02-15

    We demonstrate concentration-dependent Förster-type energy transfer in a luminescent solar concentrator (LSC) material containing two high quantum yield laser dyes in a PMMA matrix. FRET heterotransfer is shown to be approximately 50% efficient in the regime of 2×10{sup −3}molal acceptor dye by weight in the host polymer. The two dyes used have been well studied for solar concentrator applications: BASF's Lumogen Red 305, and Exciton Chemical Company's DCM both demonstrate desirable stability, quantum yield, and complementary absorption spectra. We demonstrate how multiple-dye LSC devices employing FRET increase the absorption of air mass 1.5 solar irradiance without affecting the self-absorption properties of the film. Color tunability may be achieved through the addition of additional absorbers while minimizing the impact on waveguide efficiency. -- Highlights: • Förster Resonance Energy Transfer is demonstrated in a two-dye luminescent solar concentrator. • Donor-acceptor pair distance is related to the dye concentration in PMMA. • FRET's benefit to waveguide transport losses and color tunability is discussed.

  16. Electrophoresis- and FRET-Based Measures of Serpin Polymerization.

    Science.gov (United States)

    Faull, Sarah V; Brown, Anwen E; Haq, Imran; Irving, James A

    2017-01-01

    Many serpinopathies, including alpha-1 antitrypsin (A1AT) deficiency, are associated with the formation of unbranched polymer chains of mutant serpins. In vivo, this deficiency is the result of mutations that cause kinetic or thermodynamic destabilization of the molecule. However, polymerization can also be induced in vitro from mutant or wild-type serpins under destabilizing conditions. The characteristics of the resulting polymers are dependent upon induction conditions. Due to their relationship to disease, serpin polymers, mainly those formed from A1AT, have been widely studied. Here, we describe Förster resonance energy transfer (FRET) and gel-based approaches for their characterization.

  17. Development of a Fluorescence Resonance Energy Transfer (FRET)-Based DNA Biosensor for Detection of Synthetic Oligonucleotide of Ganoderma boninense.

    Science.gov (United States)

    Mohd Bakhori, Noremylia; Yusof, Nor Azah; Abdullah, Abdul Halim; Hussein, Mohd Zobir

    2013-12-01

    An optical DNA biosensor based on fluorescence resonance energy transfer (FRET) utilizing synthesized quantum dot (QD) has been developed for the detection of specific-sequence of DNA for Ganoderma boninense, an oil palm pathogen. Modified QD that contained carboxylic groups was conjugated with a single-stranded DNA probe (ssDNA) via amide-linkage. Hybridization of the target DNA with conjugated QD-ssDNA and reporter probe labeled with Cy5 allows for the detection of related synthetic DNA sequence of Ganoderma boninense gene based on FRET signals. Detection of FRET emission before and after hybridization was confirmed through the capability of the system to produce FRET at 680 nm for hybridized sandwich with complementary target DNA. No FRET emission was observed for non-complementary system. Hybridization time, temperature and effect of different concentration of target DNA were studied in order to optimize the developed system. The developed biosensor has shown high sensitivity with detection limit of 3.55 × 10(-9) M. TEM results show that the particle size of QD varies in the range between 5 to 8 nm after ligand modification and conjugation with ssDNA. This approach is capable of providing a simple, rapid and sensitive method for detection of related synthetic DNA sequence of Ganoderma boninense.

  18. Development of a Fluorescence Resonance Energy Transfer (FRET-Based DNA Biosensor for Detection of Synthetic Oligonucleotide of Ganoderma boninense

    Directory of Open Access Journals (Sweden)

    Noremylia Mohd Bakhori

    2013-12-01

    Full Text Available An optical DNA biosensor based on fluorescence resonance energy transfer (FRET utilizing synthesized quantum dot (QD has been developed for the detection of specific-sequence of DNA for Ganoderma boninense, an oil palm pathogen. Modified QD that contained carboxylic groups was conjugated with a single-stranded DNA probe (ssDNA via amide-linkage. Hybridization of the target DNA with conjugated QD-ssDNA and reporter probe labeled with Cy5 allows for the detection of related synthetic DNA sequence of Ganoderma boninense gene based on FRET signals. Detection of FRET emission before and after hybridization was confirmed through the capability of the system to produce FRET at 680 nm for hybridized sandwich with complementary target DNA. No FRET emission was observed for non-complementary system. Hybridization time, temperature and effect of different concentration of target DNA were studied in order to optimize the developed system. The developed biosensor has shown high sensitivity with detection limit of 3.55 × 10−9 M. TEM results show that the particle size of QD varies in the range between 5 to 8 nm after ligand modification and conjugation with ssDNA. This approach is capable of providing a simple, rapid and sensitive method for detection of related synthetic DNA sequence of Ganoderma boninense.

  19. Uncovering Aberrant Mutant PKA Function with Flow Cytometric FRET

    Directory of Open Access Journals (Sweden)

    Shin-Rong Lee

    2016-03-01

    Full Text Available Biology has been revolutionized by tools that allow the detection and characterization of protein-protein interactions (PPIs. Förster resonance energy transfer (FRET-based methods have become particularly attractive as they allow quantitative studies of PPIs within the convenient and relevant context of living cells. We describe here an approach that allows the rapid construction of live-cell FRET-based binding curves using a commercially available flow cytometer. We illustrate a simple method for absolutely calibrating the cytometer, validating our binding assay against the gold standard isothermal calorimetry (ITC, and using flow cytometric FRET to uncover the structural and functional effects of the Cushing-syndrome-causing mutation (L206R on PKA’s catalytic subunit. We discover that this mutation not only differentially affects PKAcat’s binding to its multiple partners but also impacts its rate of catalysis. These findings improve our mechanistic understanding of this disease-causing mutation, while illustrating the simplicity, general applicability, and power of flow cytometric FRET.

  20. SH2 Domain-Based FRET Biosensor for Measuring BCR-ABL Activity in Living CML Cells.

    Science.gov (United States)

    Fujioka, Mari; Asano, Yumi; Nakada, Shigeyuki; Ohba, Yusuke

    2017-01-01

    Fluorescent proteins (FPs) displaying distinct spectra have shed their light on a wide range of biological functions. Moreover, sophisticated biosensors engineered to contain single or multiple FPs, including Förster resonance energy transfer (FRET)-based biosensors, spatiotemporally reveal the molecular mechanisms underlying a variety of pathophysiological processes. However, their usefulness for applied life sciences has yet to be fully explored. Recently, our research group has begun to expand the potential of FPs from basic biological research to the clinic. Here, we describe a method to evaluate the responsiveness of leukemia cells from patients to tyrosine kinase inhibitors using a biosensor based on FP technology and the principle of FRET. Upon phosphorylation of the tyrosine residue of the biosensor, binding of the SH2 domain to phosphotyrosine induces conformational change of the biosensor and brings the donor and acceptor FPs into close proximity. Therefore, kinase activity and response to kinase inhibitors can be monitored by an increase and a decrease in FRET efficiency, respectively. As in basic research, this biosensor resolves hitherto arduous tasks and may provide innovative technological advances in clinical laboratory examinations. State-of-the-art detection devices that enable such innovation are also introduced.

  1. Characteristic of fretting damage in metal material

    Energy Technology Data Exchange (ETDEWEB)

    Li, D.; Zhi, F.

    1988-10-01

    The fretting fatigue experiment of LC4 high strength aluminum alloy is described. An SEM examination of the fractology and morphology of fretting damage is carried out as well as an EDAX analysis of the chemical composition of fretting particles. The results show that many loose oxide particles were produced and accumulated in the fretting damage region. 10 references.

  2. FRET Sensor for Erythrosine Dye Based on Organic Nanoparticles: Application to Analysis of Food Stuff.

    Science.gov (United States)

    Mahajan, Prasad G; Bhopate, Dhanaji P; Kolekar, Govind B; Patil, Shivajirao R

    2016-07-01

    An aqueous suspension of fluorescent nanoparticles (PHNNPs) of naphthol based fluorescent organic compound 1-[(Z)-(2-phenylhydrazinylidene) methyl] naphthalene -2-ol (PHN) were prepared using reprecipitation method shows bathochromically shifted aggregation induced enhanced emission (AIEE) in the spectral region where erythrosine (ETS) food dye absorbs strongly. The average size of 72.6 nm of aqueous suspension of PHNNPs obtained by Dynamic light scattering results shows a narrow particle size distribution. The negative zeta potential of nano probe (-22.6 mV) responsible to adsorb oppositely charged analyte on its surface and further permit to bind nano probe and analyte within the close distance proximity required for efficient fluorescence resonance energy transfer (FRET) to take place from donor (PHNNPs) to acceptor (ETS). Systematic FRET experiments performed by measuring fluorescence quenching of PHNNPs with successive addition of ETS solution exploited the use of the PHNNPs as a novel nano probe for the detection of ETS in aqueous solution with extremely lower limit of detection equal to 3.6 nM (3.1 ng/mL). The estimation of photo kinetic and thermodynamic parameters such as quenching rate constant, enthalpy change (∆H), Gibbs free energy change (∆G) and entropy change (∆S) was obtained by the quenching results obtained at different constant temperatures which were found to fit the well-known Stern-Volmer relation. The mechanism of binding and fluorescence quenching of PHNNPs by ETS food dye is proposed on the basis of results obtained in photophysical studies, thermodynamic parameter, energy transfer efficiency, critical energy transfer distance (R0) and distance of approach between donor-acceptor molecules (r). The proposed FRET method based on fluorescence quenching of PHNNPs was successfully applied to develop an analytical method for estimation of ETS from food stuffs without interference of other complex ingredients. Graphical Abstract A

  3. Steam generator fretting-wear damage: A summary of recent findings

    International Nuclear Information System (INIS)

    Guerout, F.M.; Fisher, N.J.

    1999-01-01

    Flow-induced vibration of steam generator (SG) tubes may sometimes result in fretting-wear damage at the tube-to-support locations. Fretting-wear damage predictions are largely based on experimental data obtained at representative test conditions. Fretting-wear of SG materials has been studied at the Chalk River Laboratories for two decades. Tests are conducted in fretting-wear test machines that simulate SG environmental conditions and tube-to-support dynamic interactions. A new high-temperature force and displacement measuring system was developed to monitor tube-to-support interaction (i.e., work-rate) at operating conditions. This improvement in experimental fretting-wear technology was used to perform a comprehensive study of the effect of various environment and design parameters on SG tube wear damage. This paper summarizes the results of tests performed over the past 4 yr to study the effect of temperature, water chemistry, support geometry, and tube material on fretting-wear. The results show a significant effect of temperature on tube wear damage. Therefore, fretting-wear tests must be performed at operating temperatures in order to be relevant. No significant effect of the type of water treatment on tube wear damage was observed. For predominantly impacting motion, the wear of SG tubes in contact with 410 stainless steel is similar regardless of whether Alloy 690 or Alloy 800 is used as tubing material or whether lattice bars or broached hole supports are used. Based on results presented in this paper, an average wear coefficient value is recommended that is used for the prediction of SG tube wear depth versus time

  4. Development of device for grid spring fatigue and a cell-based fuel rod fretting wear tests

    International Nuclear Information System (INIS)

    Kim, Hyung Kyu; Yoon, Kyung Ho; Kang, Heung Seok; Song, Kee Nam

    2001-05-01

    As an activity of experimental research on the cause and the remedy of LWR fuel fretting failure, developed is test equipment for fatigue of grid spring and cell-based fuel rod fretting wear test. The equipment enables to perform the fretting wear test in the case of gap existence between spring and cladding, which has not been possible by the previously developed one (KAERI/TR-1570/2000). It can also provide fatigue test capability with the frequency of more than 10 Hz. Used are a servo-motor, an eccentric cylinder and lever mechanism for driving system as was similarly used for the previous equipment. In fretting wear test, up to 2 span-length of a fuel cladding tube can be accommodated. For fatigue test, on the other hand, a device for clamping the spring fixture is installed additionally. As a feature of the present equipment, the gap or the contacting force between a spring and a tube can be adjusted during the fretting wear test, while an initial spring force can be simulated for the fatigue test. Tests will be conducted in air at room temperature. In this report, every part of the equipment is explained with photographs, which will provide an easy understanding. Test procedure such as specimen installation, sequence of operation and program handling is also given. As a performance test of the present equipment, displacement range is measured when the hinge of the lever locates at its maximum and minimum positions. This will be used as basic information when additional eccentric cylinder is necessary for different displacement ranges

  5. Methodological considerations for global analysis of cellular FLIM/FRET measurements

    Science.gov (United States)

    Adbul Rahim, Nur Aida; Pelet, Serge; Kamm, Roger D.; So, Peter T. C.

    2012-02-01

    Global algorithms can improve the analysis of fluorescence energy transfer (FRET) measurement based on fluorescence lifetime microscopy. However, global analysis of FRET data is also susceptible to experimental artifacts. This work examines several common artifacts and suggests remedial experimental protocols. Specifically, we examined the accuracy of different methods for instrument response extraction and propose an adaptive method based on the mean lifetime of fluorescent proteins. We further examined the effects of image segmentation and a priori constraints on the accuracy of lifetime extraction. Methods to test the applicability of global analysis on cellular data are proposed and demonstrated. The accuracy of global fitting degrades with lower photon count. By systematically tracking the effect of the minimum photon count on lifetime and FRET prefactors when carrying out global analysis, we demonstrate a correction procedure to recover the correct FRET parameters, allowing us to obtain protein interaction information even in dim cellular regions with photon counts as low as 100 per decay curve.

  6. Optical bar code recognition of methyl salicylate (MES) for environmental monitoring using fluorescence resonance energy transfer (FRET) on thin films

    Science.gov (United States)

    Smith, Clint; Tatineni, Balaji; Anderson, John; Tepper, Gary

    2006-10-01

    Fluorescence resonance energy transfer (FRET) is a process in which energy is transferred nonradiatively from one fluorophore (the donor) in an excited electron state to another, the chromophore (the acceptor). FRET is distinctive in its ability to reveal the presence of specific recognition of select targets such as the nerve agent stimulant Methyl Salicylate (MES) upon spectroscopic excitation. We introduce a surface imprinted and non-imprinted thin film that underwent AC-Electrospray ionization for donor-acceptor pair(s) bound to InGaP quantum dots and mesoporous silicate nanoparticles. The donor-acceptor pair used in this investigation included MES (donor) and 6-(fluorescein-5-(and-6)- carboxamido) hexanoic acid, succinimidyl ester bound to InGaP quantum dots (acceptor). MES was then investigated as a donor to various acceptor fluorophore: InGaP: mesoporous silicate nanoparticle layers.

  7. FRET two-hybrid assay by linearly fitting FRET efficiency to concentration ratio between acceptor and donor

    Science.gov (United States)

    Du, Mengyan; Yang, Fangfang; Mai, Zihao; Qu, Wenfeng; Lin, Fangrui; Wei, Lichun; Chen, Tongsheng

    2018-04-01

    We here introduce a fluorescence resonance energy transfer (FRET) two-hybrid assay method to measure the maximal donor(D)- and acceptor(A)-centric FRET efficiency (ED,max and EA,max) of the D-A complex and its stoichiometry by linearly fitting the donor-centric FRET efficiency (ED) to the acceptor-to-donor concentration ratio (RC) and acceptor-centric FRET efficiency (EA) to 1/RC, respectively. We performed this method on a wide-field fluorescence microscope for living HepG2 cells co-expressing FRET tandem constructs and free donor/acceptor and obtained correct ED, EA, and stoichiometry values of those tandem constructs. Evaluation on the binding of Bad with Bcl-XL in Hela cells showed that Bad interacted strongly with Bcl-XL to form a Bad-Bcl-XL complex on mitochondria, and one Bad interacted mainly with one Bcl-XL molecule in healthy cells, while with multiple (maybe 2) Bcl-XL molecules in apoptotic cells.

  8. A dansyl-rhodamine chemosensor for Fe(III) based on off-on FRET

    Science.gov (United States)

    Piao, Jingyu; Lv, Jia; Zhou, Xin; Zhao, Tong; Wu, Xue

    2014-07-01

    A novel fluorescent chemosensor bearing a rhodamine and a dansyl moiety was developed for highly selective detection of Fe3+ based on fluorescence resonance energy transfer (FRET) mechanism. Binding of Fe3+ to the chemosensor induced spirolactam ring opening in the rhodamine moiety and subsequent off-on FRET from the dansyl energy donor to the rhodamine energy acceptor due to the spectral overlap between the emission of the dansyl moiety and the absorption of the ring opened rhodamine moiety. Job's plot analysis indicated a 1:1 binding stoichiometry between the chemosensor and Fe3+. The association constant was estimated to be 2.72 × 103 M-1 according to the Benesi-Hildebrand method. With the feature of easy synthesis, simple structural skeleton and excellent sensing ability, the newly synthesized chemosensor provided the potential for applying as a highly selective fluorescent probe in complex samples containing various competitive metal ions and developing other metal ion chemosensors to fulfill various needs of biological and environmental field.

  9. FRET-based biosensors for the detection and quantification of AI-2 class of quorum sensing compounds.

    Science.gov (United States)

    Rajamani, Sathish; Sayre, Richard

    2011-01-01

    Intercellular small molecular weight signaling molecules modulate a variety of biological functions in bacteria. One of the more complex behaviors mediated by intercellular signaling molecules is the suite of activities regulated by quorum sensing molecules. These molecules mediate a variety of population-dependent responses, including the expression of genes that regulate bioluminescence, type III secretion, siderophore production, colony morphology, biofilm formation, and metalloprotease production. Given their central role in regulating these responses, the detection and quantification of QS molecules has important practical implications. Until recently, the detection of QS molecules from Gram-negative bacteria has relied primarily on bacterial reporter systems. These bioassays though immensely useful are subject to interference by compounds that affect bacterial growth and metabolism. In addition, the reporter response is highly dependent on culture age and cell population density. To overcome such limitations, we developed an in vitro protein-based assay system for the rapid detection and quantification of the furanosyl borate diester (BAI-2) subclass of autoinducer-2 (AI-2) QS molecules. The biosensor is based on the interaction of BAI-2 with the Vibrio harveyi QS receptor LuxP. Conformation changes associated with BAI-2 binding to the LuxP receptor change the orientation of cyan and yellow variants of GFP (CFP and YFP) fused the N- and C-termini, respectively, of the LuxP receptor. LuxP-BAI2 binding induces changes in fluorescence resonance energy transfer (FRET) between CFP and YFP, whose magnitude of change is ligand concentration dependent. A set of ligand-insensitive LuxP-mutant FRET protein sensor was also developed for use as control biosensors. The FRET-based BAI-2 biosensor responds selectively to both synthetic and biologically derived BAI-2compounds. This report describes the use of the LuxP-FRET biosensor for the detection and quantification of

  10. Maximum likelihood-based analysis of photon arrival trajectories in single-molecule FRET

    Energy Technology Data Exchange (ETDEWEB)

    Waligorska, Marta [Adam Mickiewicz University, Faculty of Chemistry, Grunwaldzka 6, 60-780 Poznan (Poland); Molski, Andrzej, E-mail: amolski@amu.edu.pl [Adam Mickiewicz University, Faculty of Chemistry, Grunwaldzka 6, 60-780 Poznan (Poland)

    2012-07-25

    Highlights: Black-Right-Pointing-Pointer We study model selection and parameter recovery from single-molecule FRET experiments. Black-Right-Pointing-Pointer We examine the maximum likelihood-based analysis of two-color photon trajectories. Black-Right-Pointing-Pointer The number of observed photons determines the performance of the method. Black-Right-Pointing-Pointer For long trajectories, one can extract mean dwell times that are comparable to inter-photon times. -- Abstract: When two fluorophores (donor and acceptor) are attached to an immobilized biomolecule, anti-correlated fluctuations of the donor and acceptor fluorescence caused by Foerster resonance energy transfer (FRET) report on the conformational kinetics of the molecule. Here we assess the maximum likelihood-based analysis of donor and acceptor photon arrival trajectories as a method for extracting the conformational kinetics. Using computer generated data we quantify the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion (AIC) and the Bayesian information criterion (BIC) in selecting the true kinetic model. We find that the number of observed photons is the key parameter determining parameter estimation and model selection. For long trajectories, one can extract mean dwell times that are comparable to inter-photon times.

  11. Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor

    Directory of Open Access Journals (Sweden)

    Potzkei Janko

    2012-03-01

    Full Text Available Abstract Background Molecular oxygen (O2 is one of the key metabolites of all obligate and facultative aerobic pro- and eukaryotes. It plays a fundamental role in energy homeostasis whereas oxygen deprivation, in turn, broadly affects various physiological and pathophysiological processes. Therefore, real-time monitoring of cellular oxygen levels is basically a prerequisite for the analysis of hypoxia-induced processes in living cells and tissues. Results We developed a genetically encoded Förster resonance energy transfer (FRET-based biosensor allowing the observation of changing molecular oxygen concentrations inside living cells. This biosensor named FluBO (fluorescent protein-based biosensor for oxygen consists of the yellow fluorescent protein (YFP that is sensitive towards oxygen depletion and the hypoxia-tolerant flavin-binding fluorescent protein (FbFP. Since O2 is essential for the formation of the YFP chromophore, efficient FRET from the FbFP donor domain to the YFP acceptor domain only occurs in the presence but not in the absence of oxygen. The oxygen biosensor was used for continuous real-time monitoring of temporal changes of O2 levels in the cytoplasm of Escherichia coli cells during batch cultivation. Conclusions FluBO represents a unique FRET-based oxygen biosensor which allows the non-invasive ratiometric readout of cellular oxygen. Thus, FluBO can serve as a novel and powerful probe for investigating the occurrence of hypoxia and its effects on a variety of (pathophysiological processes in living cells.

  12. FRET enhancement close to gold nanoparticles positioned in DNA origami constructs.

    Science.gov (United States)

    Aissaoui, Nesrine; Moth-Poulsen, Kasper; Käll, Mikael; Johansson, Peter; Wilhelmsson, L Marcus; Albinsson, Bo

    2017-01-05

    Here we investigate the energy transfer rates of a Förster resonance energy transfer (FRET) pair positioned in close proximity to a 5 nm gold nanoparticle (AuNP) on a DNA origami construct. We study the distance dependence of the FRET rate by varying the location of the donor molecule, D, relative to the AuNP while maintaining a fixed location of the acceptor molecule, A. The presence of the AuNP induces an alteration in the spontaneous emission of the donor (including radiative and non-radiative rates) which is strongly dependent on the distance between the donor and AuNP surface. Simultaneously, the energy transfer rates are enhanced at shorter D-A (and D-AuNP) distances. Overall, in addition to the direct influence of the acceptor and AuNP on the donor decay there is also a significant increase in decay rate not explained by the sum of the two interactions. This leads to enhanced energy transfer between donor and acceptor in the presence of a 5 nm AuNP. We also demonstrate that the transfer rate in the three "particle" geometry (D + A + AuNP) depends approximately linearly on the transfer rate in the donor-AuNP system, suggesting the possibility to control FRET process with electric field induced by 5 nm AuNPs close to the donor fluorophore. It is concluded that DNA origami is a very versatile platform for studying interactions between molecules and plasmonic nanoparticles in general and FRET enhancement in particular.

  13. 48-spot single-molecule FRET setup with periodic acceptor excitation

    Science.gov (United States)

    Ingargiola, Antonino; Segal, Maya; Gulinatti, Angelo; Rech, Ivan; Labanca, Ivan; Maccagnani, Piera; Ghioni, Massimo; Weiss, Shimon; Michalet, Xavier

    2018-03-01

    Single-molecule Förster resonance energy transfer (smFRET) allows measuring distances between donor and acceptor fluorophores on the 3-10 nm range. Solution-based smFRET allows measurement of binding-unbinding events or conformational changes of dye-labeled biomolecules without ensemble averaging and free from surface perturbations. When employing dual (or multi) laser excitation, smFRET allows resolving the number of fluorescent labels on each molecule, greatly enhancing the ability to study heterogeneous samples. A major drawback to solution-based smFRET is the low throughput, which renders repetitive measurements expensive and hinders the ability to study kinetic phenomena in real-time. Here we demonstrate a high-throughput smFRET system that multiplexes acquisition by using 48 excitation spots and two 48-pixel single-photon avalanche diode array detectors. The system employs two excitation lasers allowing separation of species with one or two active fluorophores. The performance of the system is demonstrated on a set of doubly labeled double-stranded DNA oligonucleotides with different distances between donor and acceptor dyes along the DNA duplex. We show that the acquisition time for accurate subpopulation identification is reduced from several minutes to seconds, opening the way to high-throughput screening applications and real-time kinetics studies of enzymatic reactions such as DNA transcription by bacterial RNA polymerase.

  14. Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2011-01-01

    Full Text Available Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

  15. Theoretical-experimental assessment of the variables affecting fretting of Atucha I nuclear power plant utility steam generators tubes

    International Nuclear Information System (INIS)

    Kulichevsky, Raul M.

    1995-01-01

    Fretting wear of Steam Generator tubes caused by flow induced vibrations generates uncertainty on their integrity. The knowledge of the controlling variables of the wear process may give a criterion to evaluate the tubes residual life. Information on vibratory response and dynamic interaction between tubes and their supports are prerequisites for understanding the relationship between fretting wear and tube vibration. Experimental results of the vibratory response of an Atucha-I nuclear power plant type U-tube, the influence of tube/support clearance on this response and a study of tube/support dynamic interaction, which allow the verification of a finite element model of this type of tubes, are presented in this work. Also wear results for the Incoloy 800/DIN 1.4550 austenitic stainless steel pair of materials and a first evaluation of the wear constant of this pair are presented. (author)

  16. Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols.

    Directory of Open Access Journals (Sweden)

    Alexandre Bourdès

    Full Text Available Förster resonance energy transfer (FRET biosensors are powerful tools to detect biologically important ligands in real time. Currently FRET bisosensors are available for twenty-two compounds distributed in eight classes of chemicals (two pentoses, two hexoses, two disaccharides, four amino acids, one nucleobase, two nucleotides, six ions and three phytoestrogens. To expand the number of available FRET biosensors we used the induction profile of the Sinorhizobium meliloti transportome to systematically screen for new FRET biosensors.Two new vectors were developed for cloning genes for solute-binding proteins (SBPs between those encoding FRET partner fluorescent proteins. In addition to a vector with the widely used cyan and yellow fluorescent protein FRET partners, we developed a vector using orange (mOrange2 and red fluorescent protein (mKate2 FRET partners. From the sixty-nine SBPs tested, seven gave a detectable FRET signal change on binding substrate, resulting in biosensors for D-quinic acid, myo-inositol, L-rhamnose, L-fucose, β-diglucosides (cellobiose and gentiobiose, D-galactose and C4-dicarboxylates (malate, succinate, oxaloacetate and fumarate. To our knowledge, we describe the first two FRET biosensor constructs based on SBPs from Tripartite ATP-independent periplasmic (TRAP transport systems.FRET based on orange (mOrange2 and red fluorescent protein (mKate2 partners allows the use of longer wavelength light, enabling deeper penetration of samples at lower energy and increased resolution with reduced back-ground auto-fluorescence. The FRET biosensors described in this paper for four new classes of compounds; (i cyclic polyols, (ii L-deoxy sugars, (iii β-linked disaccharides and (iv C4-dicarboxylates could be developed to study metabolism in vivo.

  17. A dansyl-rhodamine chemosensor for Fe(III) based on off-on FRET.

    Science.gov (United States)

    Piao, Jingyu; Lv, Jia; Zhou, Xin; Zhao, Tong; Wu, Xue

    2014-07-15

    A novel fluorescent chemosensor bearing a rhodamine and a dansyl moiety was developed for highly selective detection of Fe(3+) based on fluorescence resonance energy transfer (FRET) mechanism. Binding of Fe(3+) to the chemosensor induced spirolactam ring opening in the rhodamine moiety and subsequent off-on FRET from the dansyl energy donor to the rhodamine energy acceptor due to the spectral overlap between the emission of the dansyl moiety and the absorption of the ring opened rhodamine moiety. Job's plot analysis indicated a 1:1 binding stoichiometry between the chemosensor and Fe(3+). The association constant was estimated to be 2.72×10(3) M(-1) according to the Benesi-Hildebrand method. With the feature of easy synthesis, simple structural skeleton and excellent sensing ability, the newly synthesized chemosensor provided the potential for applying as a highly selective fluorescent probe in complex samples containing various competitive metal ions and developing other metal ion chemosensors to fulfill various needs of biological and environmental field. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Teleseism-based Relative Time Corrections for Modern Analyses of Digitized Analog Seismograms

    Science.gov (United States)

    Lee, T. A.; Ishii, M.

    2017-12-01

    With modern-day instruments and seismic networks timed by GPS systems, synchronization of data streams is all but a forgone conclusion. However, during the analog era, when each station had its own clock, comparing data timing from different stations was a far more daunting prospect. Today, with recently developed methods by which analog data can be digitized, having the ability to accurately reconcile the timings of two separate stations would open decades worth of data to modern analyses. For example, one possible and exciting application would be using noise interferometry with digitized analog data in order to investigate changing structural features (on a volcano for example) over a much longer timescale than was previously possible. With this in mind, we introduce a new approach to sync time between stations based on teleseismic arrivals. P-wave arrivals are identified at stations for pairs of earthquakes from the digital and analog eras that have nearly identical distances, locations, and depths. Assuming accurate timing of the modern data, relative time corrections between a pair of stations can then be inferred for the analog data. This method for time correction depends upon the analog stations having modern equivalents, and both having sufficiently long durations of operation to allow for recording of usable teleseismic events. The Hawaii Volcano Observatory (HVO) network is an especially ideal environment for this, as it not only has a large and well-preserved collection of analog seismograms, but also has a long operating history (1912 - present) with many of the older stations having modern equivalents. As such, the scope of this project is to calculate and apply relative time corrections to analog data from two HVO stations, HILB (1919-present) and UWE (1928-present)(HILB now part of Pacific Tsunami network). Further application of this method could be for investigation of the effects of relative clock-drift, that is, the determining factor for how

  19. Applicability of out-of-pile fretting wear tests to in-reactor fretting wear-induced failure time prediction

    Science.gov (United States)

    Kim, Kyu-Tae

    2013-02-01

    In order to investigate whether or not the grid-to-rod fretting wear-induced fuel failure will occur for newly developed spacer grid spring designs for the fuel lifetime, out-of-pile fretting wear tests with one or two fuel assemblies are to be performed. In this study, the out-of-pile fretting wear tests were performed in order to compare the potential for wear-induced fuel failure in two newly-developed, Korean PWR spacer grid designs. Lasting 20 days, the tests simulated maximum grid-to-rod gap conditions and the worst flow induced vibration effects that might take place over the fuel life time. The fuel rod perforation times calculated from the out-of-pile tests are greater than 1933 days for 2 μm oxidized fuel rods with a 100 μm grid-to-rod gap, whereas those estimated from in-reactor fretting wear failure database may be about in the range of between 60 and 100 days. This large discrepancy in fuel rod perforation may occur due to irradiation-induced cladding oxide microstructure changes on the one hand and a temperature gradient-induced hydrogen content profile across the cladding metal region on the other hand, which may accelerate brittleness in the grid-contacting cladding oxide and metal regions during the reactor operation. A three-phase grid-to-rod fretting wear model is proposed to simulate in-reactor fretting wear progress into the cladding, considering the microstructure changes of the cladding oxide and the hydrogen content profile across the cladding metal region combined with the temperature gradient. The out-of-pile tests cannot be directly applicable to the prediction of in-reactor fretting wear-induced cladding perforations but they can be used only for evaluating a relative wear resistance of one grid design against the other grid design.

  20. Mechanisms of fretting-fatigue of titanium alloys

    Energy Technology Data Exchange (ETDEWEB)

    Antoniou, R A; Radtke, T C [Defence Sci. and Technol. Organ., Melbourne, Vic. (Australia). Aeronautical and Maritime Res. Lab.

    1997-09-30

    The effect of continuous fretting in air at 20 C on fatigue performance has been studied for Ti-17 and Ti-6Al-4V, high strength titanium alloys used for gas-turbine fan and compressor disks and blades, respectively. The effect of fretting was to reduce the fatigue stress limit from 700 MPa for plain fatigue to 200 MPa for fretting-fatigue. A number of models, supported by metallographic and fractographic evidence, are proposed which explain (i) how the cyclic loading of individual asperities results in crack initiation; (ii) the formation of multiple cracks; (iii) the existence of non-propagating cracks; and (iv) how fretting influences crack propagation once fatigue cracks have formed. (orig.) 46 refs.

  1. Simple estimation of Förster Resonance Energy Transfer (FRET) orientation factor distribution in membranes.

    Science.gov (United States)

    Loura, Luís M S

    2012-11-19

    Because of its acute sensitivity to distance in the nanometer scale, Förster resonance energy transfer (FRET) has found a large variety of applications in many fields of chemistry, physics, and biology. One important issue regarding the correct usage of FRET is its dependence on the donor-acceptor relative orientation, expressed as the orientation factor k(2). Different donor/acceptor conformations can lead to k(2) values in the 0 ≤ k(2) ≤ 4 range. Because the characteristic distance for FRET, R(0), is proportional to (k(2))1/6, uncertainties in the orientation factor are reflected in the quality of information that can be retrieved from a FRET experiment. In most cases, the average value of k(2) corresponding to the dynamic isotropic limit ( = 2/3) is used for computation of R(0) and hence donor-acceptor distances and acceptor concentrations. However, this can lead to significant error in unfavorable cases. This issue is more critical in membrane systems, because of their intrinsically anisotropic nature and their reduced fluidity in comparison to most common solvents. Here, a simple numerical simulation method for estimation of the probability density function of k(2) for membrane-embedded donor and acceptor fluorophores in the dynamic regime is presented. In the simplest form, the proposed procedure uses as input the most probable orientations of the donor and acceptor transition dipoles, obtained by experimental (including linear dichroism) or theoretical (such as molecular dynamics simulation) techniques. Optionally, information about the widths of the donor and/or acceptor angular distributions may be incorporated. The methodology is illustrated for special limiting cases and common membrane FRET pairs.

  2. Compound parabolic concentrator optical fiber tip for FRET-based fluorescent sensors

    DEFF Research Database (Denmark)

    Hassan, Hafeez Ul; Nielsen, Kristian; Aasmul, Soren

    2015-01-01

    The Compound Parabolic Concentrator (CPC) optical fiber tip shape has been proposed for intensity based fluorescent sensors working on the principle of FRET (Förster Resonance Energy Transfer). A simple numerical Zemax model has been used to optimize the CPC tip geometry for a step-index multimode...... polymer optical fiber for an excitation and emission wavelength of 550 nm and 650nm, respectively. The model suggests an increase of a factor of 1.6 to 4 in the collected fluorescent power for an ideal CPC tip, as compared to the plane-cut fiber tip for fiber lengths between 5 and 45mm...

  3. Quantitative multi-color FRET measurements by Fourier lifetime excitation-emission matrix spectroscopy

    Science.gov (United States)

    Zhao, Ming; Huang, Run; Peng, Leilei

    2012-01-01

    Förster resonant energy transfer (FRET) is extensively used to probe macromolecular interactions and conformation changes. The established FRET lifetime analysis method measures the FRET process through its effect on the donor lifetime. In this paper we present a method that directly probes the time-resolved FRET signal with frequency domain Fourier lifetime excitation-emission matrix (FLEEM) measurements. FLEEM separates fluorescent signals by their different phonon energy pathways from excitation to emission. The FRET process generates a unique signal channel that is initiated by donor excitation but ends with acceptor emission. Time-resolved analysis of the FRET EEM channel allows direct measurements on the FRET process, unaffected by free fluorophores that might be present in the sample. Together with time-resolved analysis on non-FRET channels, i.e. donor and acceptor EEM channels, time resolved EEM analysis allows precise quantification of FRET in the presence of free fluorophores. The method is extended to three-color FRET processes, where quantification with traditional methods remains challenging because of the significantly increased complexity in the three-way FRET interactions. We demonstrate the time-resolved EEM analysis method with quantification of three-color FRET in incompletely hybridized triple-labeled DNA oligonucleotides. Quantitative measurements of the three-color FRET process in triple-labeled dsDNA are obtained in the presence of free single-labeled ssDNA and double-labeled dsDNA. The results establish a quantification method for studying multi-color FRET between multiple macromolecules in biochemical equilibrium. PMID:23187535

  4. Crows spontaneously exhibit analogical reasoning.

    Science.gov (United States)

    Smirnova, Anna; Zorina, Zoya; Obozova, Tanya; Wasserman, Edward

    2015-01-19

    Analogical reasoning is vital to advanced cognition and behavioral adaptation. Many theorists deem analogical thinking to be uniquely human and to be foundational to categorization, creative problem solving, and scientific discovery. Comparative psychologists have long been interested in the species generality of analogical reasoning, but they initially found it difficult to obtain empirical support for such thinking in nonhuman animals (for pioneering efforts, see [2, 3]). Researchers have since mustered considerable evidence and argument that relational matching-to-sample (RMTS) effectively captures the essence of analogy, in which the relevant logical arguments are presented visually. In RMTS, choice of test pair BB would be correct if the sample pair were AA, whereas choice of test pair EF would be correct if the sample pair were CD. Critically, no items in the correct test pair physically match items in the sample pair, thus demanding that only relational sameness or differentness is available to support accurate choice responding. Initial evidence suggested that only humans and apes can successfully learn RMTS with pairs of sample and test items; however, monkeys have subsequently done so. Here, we report that crows too exhibit relational matching behavior. Even more importantly, crows spontaneously display relational responding without ever having been trained on RMTS; they had only been trained on identity matching-to-sample (IMTS). Such robust and uninstructed relational matching behavior represents the most convincing evidence yet of analogical reasoning in a nonprimate species, as apes alone have spontaneously exhibited RMTS behavior after only IMTS training. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Ratiometric Fluorescent Detection of Pb2+ by FRET-Based Phthalocyanine-Porphyrin Dyads.

    Science.gov (United States)

    Zhang, Dongli; Zhu, Mengliang; Zhao, Luyang; Zhang, Jinghui; Wang, Kang; Qi, Dongdong; Zhou, Yang; Bian, Yongzhong; Jiang, Jianzhuang

    2017-12-04

    Sensitive and selective detection of Pb 2+ is a very worthwhile endeavor in terms of both human health and environmental protection, as the heavy metal is fairly ubiquitous and highly toxic. In this study, we designed phthalocyanine-porphyrin (Pc-Por) heterodyads, namely, H 2 Pc-α-ZnPor (1) and H 2 Pc-β-ZnPor (2), by connecting a zinc(II) porphyrin moiety to the nonperipheral (α) or peripheral (β) position of a metal-free phthalocyanine moiety. Upon excitation at the porphyrin Soret region (420 nm), both of the dyads exhibited not only a porphyrin emission (605 nm) but also a phthalocyanine emission (ca. 700 nm), indicating the occurrence of intramolecular fluorescence resonance energy transfer (FRET) processes from the porphyrin donor to the phthalocyanine acceptor. The dyads can selectively bind Pb 2+ in the phthalocyanine core leading to a red shift of the phthalocyanine absorption and thus a decrease of spectral overlap between the porphyrin emission and phthalocyanine absorption, which in turn suppresses the intramolecular FRET. In addition, the binding of Pb 2+ can highly quench the emission of phthalocyanine by heavy-metal ion effects. The synergistic coupled functions endow the dyads with remarkable ratiometric fluorescent responses at two distinct wavelengths (F 605 /F 703 for 1 and F 605 /F 700 for 2). The emission intensity ratio increased as a linear function to the concentration of Pb 2+ in the range of 0-4.0 μM, whereas the detection limits were determined to be 3.4 × 10 -9 and 2.2 × 10 -8 M for 1 and 2, respectively. Furthermore, by comparative study of 1 and 2, the effects of distance and relative orientation between Pc and ZnPor fluorophores on the FRET efficiency and sensing performance were highlighted, which is helpful for further optimizing such FRET systems.

  6. Fast-NPS-A Markov Chain Monte Carlo-based analysis tool to obtain structural information from single-molecule FRET measurements

    Science.gov (United States)

    Eilert, Tobias; Beckers, Maximilian; Drechsler, Florian; Michaelis, Jens

    2017-10-01

    The analysis tool and software package Fast-NPS can be used to analyse smFRET data to obtain quantitative structural information about macromolecules in their natural environment. In the algorithm a Bayesian model gives rise to a multivariate probability distribution describing the uncertainty of the structure determination. Since Fast-NPS aims to be an easy-to-use general-purpose analysis tool for a large variety of smFRET networks, we established an MCMC based sampling engine that approximates the target distribution and requires no parameter specification by the user at all. For an efficient local exploration we automatically adapt the multivariate proposal kernel according to the shape of the target distribution. In order to handle multimodality, the sampler is equipped with a parallel tempering scheme that is fully adaptive with respect to temperature spacing and number of chains. Since the molecular surrounding of a dye molecule affects its spatial mobility and thus the smFRET efficiency, we introduce dye models which can be selected for every dye molecule individually. These models allow the user to represent the smFRET network in great detail leading to an increased localisation precision. Finally, a tool to validate the chosen model combination is provided. Programme Files doi:http://dx.doi.org/10.17632/7ztzj63r68.1 Licencing provisions: Apache-2.0 Programming language: GUI in MATLAB (The MathWorks) and the core sampling engine in C++ Nature of problem: Sampling of highly diverse multivariate probability distributions in order to solve for macromolecular structures from smFRET data. Solution method: MCMC algorithm with fully adaptive proposal kernel and parallel tempering scheme.

  7. Towards characterization of DNA structure under physiological conditions in vivo at the single-molecule level using single-pair FRET

    Czech Academy of Sciences Publication Activity Database

    Fessl, Tomáš; Adamec, František; Polívka, Tomáš; Foldynová-Trantírková, Silvie; Vácha, František; Trantírek, L.

    2012-01-01

    Roč. 40, č. 16 (2012), s. 10 ISSN 0305-1048 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z60220518 Keywords : in-cell FRET * fluorescence * DNA * nucleic acid * ATTO * in vivo Subject RIV: BO - Biophysics Impact factor: 8.278, year: 2012

  8. Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

    Science.gov (United States)

    Takezawa, Yusuke; Shionoya, Mitsuhiko

    2012-12-18

    With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional

  9. One-pot fabrication of FRET-based fluorescent probe for detecting copper ion and sulfide anion in 100% aqueous media

    Science.gov (United States)

    Lv, Kun; Chen, Jian; Wang, Hong; Zhang, Peisheng; Yu, Maolin; Long, Yunfei; Yi, Pinggui

    2017-04-01

    The design of effective tools for detecting copper ion (Cu2 +) and sulfide anion (S2 -) is of great importance due to the abnormal level of Cu2 + and S2 - has been associated with an increase in risk of many diseases. Herein, we report on the fabrication of fluorescence resonance energy transfer (FRET) based fluorescent probe PF (PEI-FITC) for detecting Cu2 + and S2 - in 100% aqueous media via a facile one-pot method by covalent linking fluorescein isothiocyanate (FITC) with branched-polyethylenimine (b-PEI). PF could selectively coordinate with Cu2 + among 10 metal ions to form PF-Cu2 + complex, resulting in fluorescence quenching through FRET mechanism. Furthermore, the in situ generated PF-Cu2 + complex can be used to selectively detect S2 - based on the displacement approach, resulting in an off-on type sensing. There is no obvious interference from other anions, such as Cl-, NO3-, ClO4-, SO42 -, HCO3-, CO32 -, Br-, HPO42 -, F- and S2O32 -. In addition, PF was successfully used to determine Cu2 + and S2 - in human serum and tap water samples. Therefore, the FRET-based probe PF may provide a new method for selective detection of multifarious analysts in biological and environmental applications, and even hold promise for application in more complicated systems.

  10. Hyperspectral imaging for simultaneous measurements of two FRET biosensors in pancreatic β-cells.

    Science.gov (United States)

    Elliott, Amicia D; Bedard, Noah; Ustione, Alessandro; Baird, Michelle A; Davidson, Michael W; Tkaczyk, Tomasz; Piston, David W

    2017-01-01

    Fluorescent protein (FP) biosensors based on Förster resonance energy transfer (FRET) are commonly used to study molecular processes in living cells. There are FP-FRET biosensors for many cellular molecules, but it remains difficult to perform simultaneous measurements of multiple biosensors. The overlapping emission spectra of the commonly used FPs, including CFP/YFP and GFP/RFP make dual FRET measurements challenging. In addition, a snapshot imaging modality is required for simultaneous imaging. The Image Mapping Spectrometer (IMS) is a snapshot hyperspectral imaging system that collects high resolution spectral data and can be used to overcome these challenges. We have previously demonstrated the IMS's capabilities for simultaneously imaging GFP and CFP/YFP-based biosensors in pancreatic β-cells. Here, we demonstrate a further capability of the IMS to image simultaneously two FRET biosensors with a single excitation band, one for cAMP and the other for Caspase-3. We use these measurements to measure simultaneously cAMP signaling and Caspase-3 activation in pancreatic β-cells during oxidative stress and hyperglycemia, which are essential components in the pathology of diabetes.

  11. Single-molecule three-color FRET with both negligible spectral overlap and long observation time.

    Directory of Open Access Journals (Sweden)

    Sanghwa Lee

    Full Text Available Full understanding of complex biological interactions frequently requires multi-color detection capability in doing single-molecule fluorescence resonance energy transfer (FRET experiments. Existing single-molecule three-color FRET techniques, however, suffer from severe photobleaching of Alexa 488, or its alternative dyes, and have been limitedly used for kinetics studies. In this work, we developed a single-molecule three-color FRET technique based on the Cy3-Cy5-Cy7 dye trio, thus providing enhanced observation time and improved data quality. Because the absorption spectra of three fluorophores are well separated, real-time monitoring of three FRET efficiencies was possible by incorporating the alternating laser excitation (ALEX technique both in confocal microscopy and in total-internal-reflection fluorescence (TIRF microscopy.

  12. Efficient FRET-based fuorescent ratiometric chemosensors for Fe3+ and its application in living cells

    International Nuclear Information System (INIS)

    Wang, Cuicui; Liu, Yaqi; Cheng, Junye; Song, Jianhua; Zhao, Yufen; Ye, Yong

    2015-01-01

    A series of novel FRET-based fluorescent ratiometric chemosensors (L 1 –L 6 ) were designed and synthesized. Sensor L 2 showed reversible and the best selective recognition toward Fe 3+ over other metal ions with a detection limit of 0.418 ppm, which can meet the selective requirements for practical application. Experiment results showed that the response behavior of L 2 toward Fe 3+ is pH independent in weak acid condition (pH 4.0–6.0). In addition, sensor L 2 was successfully applied for ratiometric visualization of Fe 3+ in living cells. - Highlights: • The detection limit of a new FRET probe for Fe 3+ was 0.418 ppm. • The probe exhibited high selectivity and sensitivity detection to Fe 3+ with a pH span of 4.0–6.0. • The significant changes in color could be used for naked-eye detection • The fluorescence imaging experiment demonstrated its value of practical application

  13. Probing protein-lipid interactions by FRET between membrane fluorophores

    Science.gov (United States)

    Trusova, Valeriya M.; Gorbenko, Galyna P.; Deligeorgiev, Todor; Gadjev, Nikolai

    2016-09-01

    Förster resonance energy transfer (FRET) is a powerful fluorescence technique that has found numerous applications in medicine and biology. One area where FRET proved to be especially informative involves the intermolecular interactions in biological membranes. The present study was focused on developing and verifying a Monte-Carlo approach to analyzing the results of FRET between the membrane-bound fluorophores. This approach was employed to quantify FRET from benzanthrone dye ABM to squaraine dye SQ-1 in the model protein-lipid system containing a polycationic globular protein lysozyme and negatively charged lipid vesicles composed of phosphatidylcholine and phosphatidylglycerol. It was found that acceptor redistribution between the lipid bilayer and protein binding sites resulted in the decrease of FRET efficiency. Quantification of this effect in terms of the proposed methodology yielded both structural and binding parameters of lysozyme-lipid complexes.

  14. Report on Pairing-based Cryptography.

    Science.gov (United States)

    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.

  15. Precision and accuracy in smFRET based structural studies—A benchmark study of the Fast-Nano-Positioning System

    Science.gov (United States)

    Nagy, Julia; Eilert, Tobias; Michaelis, Jens

    2018-03-01

    Modern hybrid structural analysis methods have opened new possibilities to analyze and resolve flexible protein complexes where conventional crystallographic methods have reached their limits. Here, the Fast-Nano-Positioning System (Fast-NPS), a Bayesian parameter estimation-based analysis method and software, is an interesting method since it allows for the localization of unknown fluorescent dye molecules attached to macromolecular complexes based on single-molecule Förster resonance energy transfer (smFRET) measurements. However, the precision, accuracy, and reliability of structural models derived from results based on such complex calculation schemes are oftentimes difficult to evaluate. Therefore, we present two proof-of-principle benchmark studies where we use smFRET data to localize supposedly unknown positions on a DNA as well as on a protein-nucleic acid complex. Since we use complexes where structural information is available, we can compare Fast-NPS localization to the existing structural data. In particular, we compare different dye models and discuss how both accuracy and precision can be optimized.

  16. Nuclear Fuel Fretting Mechanisms in a Room Temperature Unlubricated Condition

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young Ho; Kim, Hyung Kyu [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2008-10-15

    Recently, efforts for evaluating the fretting wear mechanism have been carried out by many researchers in various conditions. In an unlubricated condition, especially, effects of a wear debris and/or its layer on the fretting wear behavior were proposed that the formation of a well-developed glaze layer has a beneficial effect for decreasing a friction coefficient. Otherwise, a wear rate was accelerated by a third-body abrasion. At this time, it is well known that wear debris behaviors are affected by test variables such as a temperature, environment, material characteristics, etc. In a nuclear fuel fretting, however, its contact condition is quite different when compared with general fretting wear studies and could be summarized as the following; first, a fuel rod is supported by spacer grid springs and dimples that were elastically deformable. This results in a unique friction loop and a different fretting mechanism when a fuel rod is vibrated due to a flow-induced vibration (FIV). Next, it is possible that some region of the wear scar area with a specific spring shape condition could be hidden due to different wear debris behavior. So, some of the wear debris layers could be found on the worn surfaces in previous studies even though fretting wear tests were performed in a water lubricated condition. Finally, initial contact condition could be changed both an actual operating condition in power plants (i.e. high temperature and pressurized water (HTHP) under severe irradiation conditions) and the fretting wear tests for evaluating the wear resistant spring in lab conditions (i.e. from room temperature to HTHP without irradiation conditions) due to material degradations and the formation of the wear scar, respectively. In summary, the spring shape effect and the variation of the contact condition with increasing fretting cycle should be evaluated in order to improve the wear resistance of the spacer grid spring. So, in this study, fretting wear tests have been

  17. Spin contamination analogy, Kramers pairs symmetry and spin density representations at the 2-component unrestricted Hartree-Fock level of theory

    KAUST Repository

    Bučinský , Luká š; Malček, Michal; Biskupič, Stanislav; Jayatilaka, Dylan; Bü chel, Gabriel E.; Arion, Vladimir B.

    2015-01-01

    "Kramers pairs symmetry breaking" is evaluated at the 2-component (2c) Kramers unrestricted and/or general complex Hartree-Fock (GCHF) level of theory, and its analogy with "spin contamination" at the 1-component (1c) unrestricted Hartree-Fock (UHF

  18. Fretting-wear damage of heat exchanger tubes: a proposed damage criterion based on tube vibration response

    International Nuclear Information System (INIS)

    Yetisir, M.; McKerrow, E.; Pettigrew, M.J.

    1997-01-01

    A simple criterion is proposed to estimate fretting-wear damage in heat exchanger tubes with clearance supports. The criterion is based on parameters such as vibration frequency, mid-span vibration amplitude, span length, tube mass and an empirical wear coefficient. It is generally accepted that fretting-wear damage is proportional to a parameter called work-rate. Work-rate is a measure of the dynamic interaction between a vibrating tube and its supports. Due to the complexity of the impact-sliding behavior at the clearance-supports, work-rate calculations for heat exchanger tubes require specialized non-linear finite element codes. These codes include contact models for various clearance-support geometries. Such non-linear finite element analyses are complex, expensive and time consuming. The proposed criterion uses the results of linear vibration analysis (i.e., vibration frequency and mid-span vibration amplitude due to turbulence) and does not require a non-linear analysis. It can be used by non-specialists for a quick evaluation of the expected work-rate, and hence, the fretting-wear damage of heat exchanger tubes. The proposed criterion was obtained from an extensive parametric study that was conducted using a non-linear finite element program. It is shown that, by using the proposed work-rate criteria, work-rate can be estimated within a factor of two. This result, however, requires further testing with more complicated flow patterns. (author)

  19. The Leakage determination on corrosion fretting machine

    International Nuclear Information System (INIS)

    Sriyono; Satmoko, Ari; Hafid, Abdul; Febrianto; Prasetio, Joko; Abtokhi; Sumarno, Edy; Handoyo, Ismu; Hidayati, Nur Rahmah; Histori

    1998-01-01

    Fretting machine is an experimental loop to learn fretting corrosion phenomena wich is caused by loading and vibration. On the steam generator, one of the corrosion process that's occurred, it can be caused by vibration between tubes and bending material. Because of high flow rate inside the tube, the high frequency vibration will appeared so it can make the corrosion on bending material more faster. This process can be simulate by fretting machine. This machine has already damage because of leakage. So it will be repaired by dismantling, radiography testing and redrawing. from the result of radiography, the leakage is caused by cracking on bellows seals of the dynamic main support

  20. Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening.

    Science.gov (United States)

    Doucette, Jaimee; Zhao, Ziyan; Geyer, Rory J; Barra, Melanie M; Balunas, Marcy J; Zweifach, Adam

    2016-07-01

    Genetically encoded sensors based on intramolecular FRET between CFP and YFP are used extensively in cell biology research. Flow cytometry has been shown to offer a means to measure CFP-YFP FRET; we suspected it would provide a unique way to conduct multiplexed measurements from cells expressing different FRET sensors, which is difficult to do with microscopy, and that this could be used for screening. We confirmed that flow cytometry accurately measures FRET signals using cells transiently transfected with an ERK activity reporter, comparing responses measured with imaging and cytometry. We created polyclonal long-term transfectant lines, each expressing a different intramolecular FRET sensor, and devised a way to bar-code four distinct populations of cells. We demonstrated the feasibility of multiplexed measurements and determined that robust multiplexed measurements can be conducted in plate format. To validate the suitability of the method for screening, we measured responses from a plate of bacterial extracts that in unrelated experiments we had determined contained the protein kinase C (PKC)-activating compound teleocidin A-1. The multiplexed assay correctly identifying the teleocidin A-1-containing well. We propose that multiplexed cytometric FRET measurements will be useful for analyzing cellular function and for screening compound collections. © 2016 Society for Laboratory Automation and Screening.

  1. TECHNIQUE OF TESTING ON FRETTING AT THE SPHERE-TO-PLANE CONTACT

    Directory of Open Access Journals (Sweden)

    А. Khimko

    2012-12-01

    Full Text Available  The methodology of conducting tests on fretting at the sphere-to-plane contact was developed for the wing mechanization unit, namely for screw-nut pair with intermediate balls. Wearability tests were conducted on a modified installation МФК-1, the feature of which is the designed holder that allows testing with real balls. It was found that at the dry contact of ШХ-15 and 30Х2НВФA materials, surface microcracks are formed due to welding of microasperities areas and their rupture under the influence of vibration.

  2. A rhodamine–dansyl conjugate as a FRET based sensor for Fe{sup 3+} in the red spectral region

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Puhui, E-mail: pxie2007@yahoo.com.cn [College of Sciences, Henan Agricultural University, Zhengzhou 450002 (China); Guo, Fengqi, E-mail: fqguo@zzu.edu.cn [College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001 (China); Xia, Ruirui; Wang, Yao [College of Sciences, Henan Agricultural University, Zhengzhou 450002 (China); Yao, Denghui [College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001 (China); Yang, Guoyu; Xie, Lixia [College of Sciences, Henan Agricultural University, Zhengzhou 450002 (China)

    2014-01-15

    A new fluorescent resonance energy transfer (FRET) based fluorescent probe (compound 1) containing a dansyl unit as a donor and rhodamine 101 as an acceptor was developed to detect Fe{sup 3+} from other transition metal ions through ratiometric sensing in organic-aqueous solutions. Fe{sup 3+} induced a ring-opening reaction of the spirolactam rhodamine moiety of 1 resulting in the formation of a fluorescent derivative that can serve as the FRET acceptor. Ratiometric sensing of Fe{sup 3+} was accomplished by plotting the fluorescence intensity ratio at 605 nm and 515 nm versus ferric ion concentration. The probe displayed a linear response to Fe{sup 3+} in the range of 5.5–25 μM with a detection limit of 0.64 μM. A 1:1 stoichiometry for the 1–Fe{sup 3+} complex was formed with an association constant of 1.74×10{sup 4} M{sup −1}. The probe also exhibited a large Stokes shift (225 nm) which can eliminate backscattering effects of excitation light. -- Highlights: • A new colorimetric and fluorescent “off–on” chemosensor for Fe{sup 3+} was synthesized. • It can respond to Fe{sup 3+} in the red spectral region based on a FRET mechanism. • Its ratiometric sensing for Fe{sup 3+} can be accomplished with a signal to noise ratio of 214. • The large Stokes shift (225 nm) can rule out the excitation backscattering effects.

  3. Fretting wear characteristic tests of X2-GEN midgrid for SMART under a FIV rod trace

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young Ho; Lee, Kang Hee; Kim, Jae Yong; Kim, Hyung Kyu [KAERI, Daejeon (Korea, Republic of)

    2011-12-15

    The KEPCO Nuclear Fuel Co. requested the fretting wear characteristic tests of a X2-GEN midgrid under a FIV rod trace at room temperature air. The following results were obtained for the fretting wear test. {center_dot} Fretting wear tests under a FIV rod trace Based on the result of the fretting wear tests of the X2-GEN and 17ACE7 1x1 mid-grid under a FIV rod trace, X2-GEN mid-grid showed a slightly severe wear volume rather than 17ACE7 spring. But, maximum wear depth shows an opposite behavior. This is due to spring shape effect. The fretting wear mechanisms at each mid-grid were influenced by each spring shape, that are depended on the different impacting behavior under a FIV rod motion. Up to 5x105 cycles, wear characteristics of each mid-grid shows a relatively similar wear rate. Consequently, it is necessary to further study for examining exact fretting wear behavior under a FIV rod tra

  4. Fretting fatigue behavior of high-strength steel monostrands under bending load

    DEFF Research Database (Denmark)

    Winkler, Jan; Georgakis, Christos T.; Fischer, Gregor

    2015-01-01

    In this paper, the fretting fatigue behavior of pretensioned high-strength steel monostrands is investigated. To measure the local deformations on the strands, a novel method based on the digital image correlation (DIC) technique was used to quantify the relative movement between individual wires...... along the length of the monostrand. Information about the monostrand bending stiffness and the extent of relative displacement between core and outer wires of a monostrand undergoing flexural deformations is provided. From the series of dynamic fatigue tests, a fretting fatigue spectrum is derived...

  5. a Study on the Fretting Fatigue Life of Zircaloy Alloys

    Science.gov (United States)

    Kwon, Jae-Do; Park, Dae-Kyu; Woo, Seung-Wan; Chai, Young-Suck

    Studies on the strength and fatigue life of machines and structures have been conducted in accordance with the development of modern industries. In particular, fine and repetitive cyclic damage occurring in contact regions has been known to have an impact on fretting fatigue fractures. The main component of zircaloy alloy is Zr, and it possesses good mechanical characteristics at high temperatures. This alloy is used in the fuel rod material of nuclear power plants because of its excellent resistance. In this paper, the effect of the fretting damage on the fatigue behavior of the zircaloy alloy is studied. Further, various types of mechanical tests such as tension and plain fatigue tests are performed. Fretting fatigue tests are performed with a flat-flat contact configuration using a bridge-type contact pad and plate-type specimen. Through these experiments, it is found that the fretting fatigue strength decreases by about 80% as compared to the plain fatigue strength. Oblique cracks are observed in the initial stage of the fretting fatigue, in which damaged areas are found. These results can be used as the basic data for the structural integrity evaluation of corrosion-resisting alloys considering the fretting damages.

  6. Understanding and modeling Förster-type resonance energy transfer (FRET)

    CERN Document Server

    Hernández Martínez, Pedro Ludwig; Demir, Hilmi Volkan

    2017-01-01

    This Brief presents a complete study of the generalized theory of Förster-type energy transfer in nanostructures with mixed dimensionality. Here the aim is to obtain a generalized theory of FRET including a comprehensive set of analytical equations for all combinations and configurations of nanostructures and deriving generic expressions for the dimensionality involved. In this brief, the modification of FRET mechanism with respect to the nanostructure serving as the donor vs. the acceptor will be included, focusing on the rate’s distance dependency and the role of the effective dielectric function in FRET, which will be a unique, useful source for those who study and model FRET.

  7. CONSIDERATIONS REGARDING THE FRETTING PHENOMENON USING LEAF SPRINGS

    Directory of Open Access Journals (Sweden)

    Stefan GHIMIȘI

    2015-05-01

    Full Text Available The fretting phenomenon represents particulary and complex form of wear who is; generaly, and/or weary of fretting who is produced on the load contact in a relative oscialatory movement lay small amplitude.A simultaneoustly applied tangential force and normal into contact appears a adhesion force

  8. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.

    Directory of Open Access Journals (Sweden)

    Michael F Sloma

    2017-11-01

    Full Text Available Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package.

  9. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.

    Science.gov (United States)

    Sloma, Michael F; Mathews, David H

    2017-11-01

    Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package.

  10. Prediction of pressure tube fretting-wear damage due to fuel vibration

    International Nuclear Information System (INIS)

    Yetisir, M.; Fisher, N.J.

    1997-01-01

    Fretting marks between fuel bundle bearing pads and pressure tubes have been observed at the inlet end of some Darlington Nuclear Generating Station (NGS) and Bruce NGS fuel channels. The excitation mechanisms that lead to fretting are not fully understood. In this paper, the possibility of bearing pad-to-pressure tube fretting due to turbulence-induced motion of the fuel element is investigated. Numerical simulations indicate that this mechanism by itself is not likely to cause the level of fretting experienced in Darlington and Bruce NGSs. (orig.)

  11. Development of FRET biosensors for mammalian and plant systems

    NARCIS (Netherlands)

    Hamers, D.; van Voorst Vader, L.; Borst, J.W.; Goedhart, J.

    2014-01-01

    Genetically encoded biosensors are increasingly used in visualising signalling processes in different organisms. Sensors based on green fluorescent protein technology are providing a great opportunity for using Forster resonance energy transfer (FRET) as a tool that allows for monitoring dynamic

  12. A Study on Surface Modification of Al7075-T6 Alloy against Fretting Fatigue Phenomenon

    Directory of Open Access Journals (Sweden)

    E. Mohseni

    2014-01-01

    Full Text Available Aircraft engines, fuselage, automobile parts, and energy saving strategies in general have promoted the interest and research in the field of lightweight materials, typically on alloys based on aluminum. Aluminum alloy itself does not have suitable wear resistance; therefore, it is necessary to enhance surface properties for practical applications, particularly when aluminum is in contact with other parts. Fretting fatigue phenomenon occurs when two surfaces are in contact with each other and one or both parts are subjected to cyclic load. Fretting drastically decreases the fatigue life of materials. Therefore, investigating the fretting fatigue life of materials is an important subject. Applying surface modification methods is anticipated to be a supreme solution to gradually decreasing fretting damage. In this paper, the authors would like to review methods employed so far to diminish the effect of fretting on the fatigue life of Al7075-T6 alloy. The methods include deep rolling, shot peening, laser shock peening, and thin film hard coatings. The surface coatings techniques are comprising physical vapor deposition (PVD, hard anodizing, ion-beam-enhanced deposition (IBED, and nitriding.

  13. Detecting analogies unconsciously

    Directory of Open Access Journals (Sweden)

    Thomas Peter Reber

    2014-01-01

    Full Text Available Analogies may arise from the conscious detection of similarities between a present and a past situation. In this functional magnetic resonance imaging study, we tested whether young volunteers would detect analogies unconsciously between a current supraliminal (visible and a past subliminal (invisible situation. The subliminal encoding of the past situation precludes awareness of analogy detection in the current situation. First, participants encoded subliminal pairs of unrelated words in either one or nine encoding trials. Later, they judged the semantic fit of supraliminally presented new words that either retained a previously encoded semantic relation (‘analog’ or not (‘broken analog’. Words in analogs versus broken analogs were judged closer semantically, which reflects unconscious analogy detection. Hippocampal activity associated with subliminal encoding correlated with the behavioral measure of unconscious analogy detection. Analogs versus broken analogs were processed with reduced prefrontal but enhanced medial temporal activity. We conclude that analogous episodes can be detected even unconsciously drawing on the episodic memory network.

  14. Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-08-01

    Full Text Available The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I and 2'-deoxyribo-2,6-diaminopurine (D as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G•C > D•T ≈ I•C > A•T > G•T > I•T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

  15. FLIM-FRET image analysis of tryptophan in prostate cancer cells

    Science.gov (United States)

    Periasamy, Ammasi; Alam, Shagufta R.; Svindrych, Zdenek; Wallrabe, Horst

    2017-07-01

    A region of interest (ROI) based quantitative FLIM-FRET image analysis is developed to quantitate the autofluorescence signals of the essential amino acid tryptophan as a biomarker to investigate the metabolism in prostate cancer cells.

  16. Analogical reasoning and prefrontal cortex: evidence for separable retrieval and integration mechanisms.

    Science.gov (United States)

    Bunge, Silvia A; Wendelken, Carter; Badre, David; Wagner, Anthony D

    2005-03-01

    The present study examined the contributions of prefrontal cortex (PFC) subregions to two component processes underlying verbal analogical reasoning: semantic retrieval and integration. Event-related functional magnetic resonance imaging data were acquired while subjects performed propositional analogy and semantic decision tasks. On each trial, subjects viewed a pair of words (pair 1), followed by an instructional cue and a second word pair (pair 2). On analogy trials, subjects evaluated whether pair 2 was semantically analogous to pair 1. On semantic trials, subjects indicated whether the pair 2 words were semantically related to each other. Thus, analogy--but not semantic--trials required integration across multiple retrieved relations. To identify regions involved in semantic retrieval, we manipulated the associative strength of pair 1 words in both tasks. Anterior left inferior PFC (aLIPC) was modulated by associative strength, consistent with a role in controlled semantic retrieval. Left frontopolar cortex was insensitive to associative strength, but was more sensitive to integration demands than was aLIPC, consistent with a role in integrating the products of semantic retrieval to evaluate whether distinct representations are analogous. Right dorsolateral PFC exhibited a profile consistent with a role in response selection rather than retrieval or integration. These findings indicate that verbal analogical reasoning depends on multiple, PFC-mediated computations.

  17. Low-voltage analog front-end processor design for ISFET-based sensor and H+ sensing applications

    Science.gov (United States)

    Chung, Wen-Yaw; Yang, Chung-Huang; Peng, Kang-Chu; Yeh, M. H.

    2003-04-01

    This paper presents a modular-based low-voltage analog-front-end processor design in a 0.5mm double-poly double-metal CMOS technology for Ion Sensitive Field Effect Transistor (ISFET)-based sensor and H+ sensing applications. To meet the potentiometric response of the ISFET that is proportional to various H+ concentrations, the constant-voltage and constant current (CVCS) testing configuration has been used. Low-voltage design skills such as bulk-driven input pair, folded-cascode amplifier, bootstrap switch control circuits have been designed and integrated for 1.5V supply and nearly rail-to-rail analog to digital signal processing. Core modules consist of an 8-bit two-step analog-digital converter and bulk-driven pre-amplifiers have been developed in this research. The experimental results show that the proposed circuitry has an acceptable linearity to 0.1 pH-H+ sensing conversions with the buffer solution in the range of pH2 to pH12. The processor has a potential usage in battery-operated and portable healthcare devices and environmental monitoring applications.

  18. Prediction of pressure tube fretting-wear damage due to fuel vibration

    Energy Technology Data Exchange (ETDEWEB)

    Yetisir, M; Fisher, N J [Atomic Energy of Canada Ltd., Chalk River, ON (Canada)

    1996-12-31

    Fretting marks between fuel bundle bearing pads and pressure tubes have been observed at the inlet end of some Darlington NGS (nuclear generating station) and Bruce NGS fuel channels. The excitation mechanisms that lead to fretting are not fully understood. In this paper, the possibility of bearing pad-to-pressure tube fretting due to turbulence-induced motion of the fuel element is investigated. Numerical simulations indicate that this mechanism by itself is not likely to cause the level of fretting experienced in Darlington and Bruce NGS`s (nuclear generating stations). (author). 12 refs., 2 tabs., 11 figs.

  19. Design improvement for fretting-wear reduction of HANARO fuel assembly

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Yeong Garp; Chae, H. T.; Ryu, J. S.; Kim, H. R

    2000-06-01

    In the course of the visual inspection of the fuel assemblies un-loaded from the reactor core in December 1996, it was observed that many of fuel assemblies had mechanical damages on some components. The major damage was the freting-wear on spacer plates and endplates due to the flow induced vibration of the fuel assembly in the flow tube. Since the reactor is activated and the system modification for complete removal of the driving factors of the vibration of fuel assemblies is practically very difficult, the focus has been on the design change of the fuel assemblies. Consequently, various design changes were proposed to strengthen the wear resistance of the components based on the evaluation of the visual inspection results. The validity of the proposals was verified through the performance tests for the modified components, and the vibration test and endurance test for the fuel assemblies using the single-channel test rig(SCTR) in AECL.The subsequent design changes were additionally proposed based on the visual inspections for the fuel assemblies that had been fabricated according to the first design change and loaded in the core. As the effects of the first design change, the fretting-wear of spacer plates was remarkably reduced and the period until fretting-wear damage was extended by 60% for the first modified 36-rod fuel assembly. It is too early to say the endurance life time for the first modified 18-rod fuel assembly because of insufficient statistical data of only two bundles damaged, but the fretting-wear at the bottom endplate slot was reduced to about 50%. The second modified fuel assemblies, that were not loaded into the core yet, are expected to meet the design requirements for the core residence time due to strengthening the weak parts from the fretting-wear point of view. This report describes design changes and tests for fuel assemblies of HANARO to reduce the fretting-wear, and estimates the effects of design improvement quantitatively compared

  20. Design improvement for fretting-wear reduction of HANARO fuel assembly

    International Nuclear Information System (INIS)

    Cho, Yeong Garp; Chae, H. T.; Ryu, J. S.; Kim, H. R.

    2000-06-01

    In the course of the visual inspection of the fuel assemblies un-loaded from the reactor core in December 1996, it was observed that many of fuel assemblies had mechanical damages on some components. The major damage was the freting-wear on spacer plates and endplates due to the flow induced vibration of the fuel assembly in the flow tube. Since the reactor is activated and the system modification for complete removal of the driving factors of the vibration of fuel assemblies is practically very difficult, the focus has been on the design change of the fuel assemblies. Consequently, various design changes were proposed to strengthen the wear resistance of the components based on the evaluation of the visual inspection results. The validity of the proposals was verified through the performance tests for the modified components, and the vibration test and endurance test for the fuel assemblies using the single-channel test rig(SCTR) in AECL.The subsequent design changes were additionally proposed based on the visual inspections for the fuel assemblies that had been fabricated according to the first design change and loaded in the core. As the effects of the first design change, the fretting-wear of spacer plates was remarkably reduced and the period until fretting-wear damage was extended by 60% for the first modified 36-rod fuel assembly. It is too early to say the endurance life time for the first modified 18-rod fuel assembly because of insufficient statistical data of only two bundles damaged, but the fretting-wear at the bottom endplate slot was reduced to about 50%. The second modified fuel assemblies, that were not loaded into the core yet, are expected to meet the design requirements for the core residence time due to strengthening the weak parts from the fretting-wear point of view. This report describes design changes and tests for fuel assemblies of HANARO to reduce the fretting-wear, and estimates the effects of design improvement quantitatively compared

  1. FRET-based binding assay between a fluorescent cAMP analogue and a cyclic nucleotide-binding domain tagged with a CFP.

    Science.gov (United States)

    Romero, Francisco; Santana-Calvo, Carmen; Sánchez-Guevara, Yoloxochitl; Nishigaki, Takuya

    2017-09-01

    The cyclic nucleotide-binding domain (CNBD) functions as a regulatory domain of many proteins involved in cyclic nucleotide signalling. We developed a straightforward and reliable binding assay based on intermolecular fluorescence resonance energy transfer (FRET) between an adenosine-3', 5'-cyclic monophosphate analogue labelled with fluorescein and a recombinant CNBD of human EPAC1 tagged with a cyan fluorescence protein (CFP). The high FRET efficiency of this method (~ 80%) allowed us to perform several types of binding experiments with nanomolar range of sample using conventional equipment. In addition, the CFP tag on the CNBD enabled us to perform a specific binding experiment using an unpurified protein. Considering these advantages, this technique is useful to study poorly characterized CNBDs. © 2017 Federation of European Biochemical Societies.

  2. Surveillance of siRNA integrity by FRET imaging

    Science.gov (United States)

    Järve, Anne; Müller, Julius; Kim, Il-Han; Rohr, Karl; MacLean, Caroline; Fricker, Gert; Massing, Ulrich; Eberle, Florian; Dalpke, Alexander; Fischer, Roger; Trendelenburg, Michael F.; Helm, Mark

    2007-01-01

    Techniques for investigation of exogenous small interfering RNA (siRNA) after penetration of the cell are of substantial interest to the development of efficient transfection methods as well as to potential medical formulations of siRNA. A FRET-based visualization method including the commonplace dye labels fluorescein and tetramethylrhodamin (TMR) on opposing strands of siRNA was found compatible with RNA interference (RNAi). Investigation of spectral properties of three labelled siRNAs with differential FRET efficiencies in the cuvette, including pH dependence and FRET efficiency in lipophilic environments, identified the ratio of red and green fluorescence (R/G-ratio) as a sensitive parameter, which reliably identifies samples containing >90% un-degraded siRNA. Spectral imaging of siRNAs microinjected into cells showed emission spectra indistinguishable from those measured in the cuvette. These were used to establish a calibration curve for assessing the degradation state of siRNA in volume elements inside cells. An algorithm, applied to fluorescence images recorded in standard green and red fluorescence channels, produces R/G-ratio images of high spatial resolution, identifying volume elements in the cell with high populations of intact siRNA with high fidelity. To demonstrate the usefulness of this technique, the movement of intact siRNA molecules are observed after introduction into the cytosol by microinjection, standard transfection and lipofection with liposomes. PMID:17890733

  3. Producing and Recognizing Analogical Relations

    Science.gov (United States)

    Lipkens, Regina; Hayes, Steven C

    2009-01-01

    Analogical reasoning is an important component of intelligent behavior, and a key test of any approach to human language and cognition. Only a limited amount of empirical work has been conducted from a behavior analytic point of view, most of that within Relational Frame Theory (RFT), which views analogy as a matter of deriving relations among relations. The present series of four studies expands previous work by exploring the applicability of this model of analogy to topography-based rather than merely selection-based responses and by extending the work into additional relations, including nonsymmetrical ones. In each of the four studies participants pretrained in contextual control over nonarbitrary stimulus relations of sameness and opposition, or of sameness, smaller than, and larger than, learned arbitrary stimulus relations in the presence of these relational cues and derived analogies involving directly trained relations and derived relations of mutual and combinatorial entailment, measured using a variety of productive and selection-based measures. In Experiment 1 participants successfully recognized analogies among stimulus networks containing same and opposite relations; in Experiment 2 analogy was successfully used to extend derived relations to pairs of novel stimuli; in Experiment 3 the procedure used in Experiment 1 was extended to nonsymmetrical comparative relations; in Experiment 4 the procedure used in Experiment 2 was extended to nonsymmetrical comparative relations. Although not every participant showed the effects predicted, overall the procedures occasioned relational responses consistent with an RFT account that have not yet been demonstrated in a behavior-analytic laboratory setting, including productive responding on the basis of analogies. PMID:19230515

  4. Genome-wide screening for genes whose deletions confer sensitivity to mutagenic purine base analogs in yeast

    Directory of Open Access Journals (Sweden)

    Kozmin Stanislav G

    2005-06-01

    Full Text Available Abstract Background N-hydroxylated base analogs, such as 6-hydroxylaminopurine (HAP and 2-amino-6-hydroxylaminopurine (AHA, are strong mutagens in various organisms due to their ambiguous base-pairing properties. The systems protecting cells from HAP and related noncanonical purines in Escherichia coli include specialized deoxyribonucleoside triphosphatase RdgB, DNA repair endonuclease V, and a molybdenum cofactor-dependent system. Fewer HAP-detoxification systems have been identified in yeast Saccharomyces cerevisiae and other eukaryotes. Cellular systems protecting from AHA are unknown. In the present study, we performed a genome-wide search for genes whose deletions confer sensitivity to HAP and AHA in yeast. Results We screened the library of yeast deletion mutants for sensitivity to the toxic and mutagenic action of HAP and AHA. We identified novel genes involved in the genetic control of base analogs sensitivity, including genes controlling purine metabolism, cytoskeleton organization, and amino acid metabolism. Conclusion We developed a method for screening the yeast deletion library for sensitivity to the mutagenic and toxic action of base analogs and identified 16 novel genes controlling pathways of protection from HAP. Three of them also protect from AHA.

  5. Highly sensitive FRET-based fluorescence immunoassay for aflatoxin B1 using cadmium telluride quantum dots

    International Nuclear Information System (INIS)

    Zekavati, Roya; Bayat, Mansour; Safi, Shahabeddin; Hashemi, Seyed Jamal; Rahmani-Cherati, Tavoos; Tabatabaei, Meisam; Mohsenifar, Afshin

    2013-01-01

    We report on a competitive immunoassay for the determination of aflatoxin B1 using fluorescence resonance energy transfer (FRET) from anti-aflatoxin B1 antibody (immobilized on the shell of CdTe quantum dots) to Rhodamine 123 (Rho 123-labeled aflatoxin B1 bound to albumin). The highly specific immuno reaction between the antibody against aflatoxin B1 on the QDs and the labeled-aflatoxin B1 brings the Rho 123 fluorophore (acting as the acceptor) and the QDs (acting as the donor) in close spatial proximity and causes FRET to occur upon photoexcitation of the QDs. In the absence of unlabeled aflatoxin B1, the antigen-antibody complex is stable, and strong emission resulting from the FRET from QDs to labeled aflatoxin B1 is observed. In the presence of aflatoxin B1, it will compete with the labeled aflatoxin B1-albumin complex for binding to the antibody-QDs conjugate so that FRET will be increasingly suppressed. The reduction in the fluorescence intensity of the acceptor correlates well with the concentration of aflatoxin B1. The feasibility of the method was established by the detection of aflatoxin B1 in spiked human serum. There is a linear relationship between the increased fluorescence intensity of Rho 123 with increasing concentration of aflatoxin B1 in spike human serum, over the range of 0.1–0.6 μmol·mL −1 . The limit of detection is 2 × 10 −11 M. This homogeneous competitive detection scheme is simple, rapid and efficient, and does not require excessive washing and separation steps. (author)

  6. Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints.

    Science.gov (United States)

    Awale, Mahendra; Jin, Xian; Reymond, Jean-Louis

    2015-01-01

    Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch and should provide useful assistance to drug

  7. Sensitivity-Enhancement of FRET Immunoassays by Multiple-Antibody Conjugation on Quantum Dots.

    Science.gov (United States)

    Annio, Giacomo; Jennings, Travis; Tagit, Oya; Hildebrandt, Niko

    2018-05-23

    Quantum dots (QDs) are not only advantageous for color-tuning, improved brightness, and high stability, but their nanoparticle surfaces also allow for the attachment of many biomolecules. Because IgG antibodies (ABs) are in the same size range of biocompatible QDs and the AB orientation after conjugation to the QD is often random, it is difficult to predict if few or many ABs per QD will lead to an efficient AB-QD conjugate. This is particularly true for homogeneous Förster resonance energy transfer (FRET) sandwich immunoassays, for which the ABs on the QD must bind a biomarker that needs to bind a second AB-FRET-conjugate. Here, we investigate the performance of Tb-to-QD FRET immunoassays against total prostate specific antigen (TPSA) by changing the number of ABs per QD while leaving all the other assay components unchanged. We first characterize the AB-QD conjugation by various spectroscopic, microscopic, and chromatographic techniques and then quantify the TPSA immunoassay performance regarding sensitivity, limit of detection, and dynamic range. Our results show that an increasing conjugation ratio leads to significantly enhanced FRET immunoassays. These findings will be highly important for developing QD-based immunoassays in which the concentrations of both ABs and QDs can significantly influence the assay performance.

  8. FRET Response of a Modified Ribose Receptor Expressed in the Diatom Thalassiosira pseudonana

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Hanna

    2011-08-26

    The ability to insert complex proteins into silica has many applications including biosensing. Previous research has demonstrated how to direct proteins to the biosilica of diatoms [1]. Here, we show that a complex fusion protein that includes an enzyme, a bacterial ribose periplasmic binding protein, flanked by fluorescent proteins constituting a FRET pair can remain functional in the frustules of living diatoms. A Sil3 tag is attached to the N-terminal end to localize the fusion protein to frustules of the diatom Thalassiosira pseudonana. When ribose was applied, a larger decrease in FRET response was seen in transformed cells than in untransformed cells. Multiple forms of the expression vector were tested to find the optimal system; specifically, a one-vector system was compared to a two-vector system and the gDNA version of the Sil3 localization tag was compared to the cDNA version. The optimal system was found to be a one-vector system with the genomic version of the Sil3 tag to direct the protein to the frustules. Localization of the enzyme to the frustules was further confirmed through cell fluorescence imaging.

  9. A Study on Fretting Behavior in Room Temperature for Inconel Alloy 690

    Science.gov (United States)

    Kwon, Jae Do; Chai, Young Suck; Bae, Yong Tak; Choi, Sung Jong

    The initial crack under fretting condition occurs at lower stress amplitude and lower cycles of cyclic loading than that under plain fatigue condition. The fretting damage, for example, can be observed in fossil and nuclear power plant, aircraft, automobile and petroleum chemical plants etc. INCONEL alloy 690 is a high-chromium nickel alloy having excellent resistance to many corrosive aqueous media and high-temperature atmospheres. This alloy is used extensively in the industries of nuclear power, chemicals, heat-treatment and electronics. In this paper, the effect of fretting damage on fatigue behavior for INCONEL alloy 690 was studied. Also, various kinds of tests on mechanical properties such as hardness, tension and plain fatigue tests are performed. Fretting fatigue tests were carried out with flat-flat contact configuration using a bridge type contact pad and plate type specimen. Through these experiments, it is found that the fretting fatigue strength decreased about 43% compared to the plain fatigue strength. In fretting fatigue, the wear debris is observed on the contact surface, and the oblique micro-cracks are initiated at an earlier stage. These results can be used as the basic data in a structural integrity evaluation of heat and corrosion resistant alloy considering fretting damages.

  10. Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET

    NARCIS (Netherlands)

    Hohlbein, J.; Kapanidis, A.N.

    2016-01-01

    Monitoring conformational changes in DNA polymerases using single-molecule Förster resonance energy transfer (smFRET) has provided new tools for studying fidelity-related mechanisms that promote the rejection of incorrect nucleotides before DNA synthesis. In addition to the previously known open

  11. Fuel bundle to pressure tube fretting in Bruce and Darlington

    Energy Technology Data Exchange (ETDEWEB)

    Norsworthy, A G; Ditschun, A [Atomic Energy of Canada Ltd., Mississauga, ON (Canada)

    1996-12-31

    As the fuel channel elongates due to creep, the fuel string moves relative to the inlet until the fuel pads at the inboard end eventually separate from the spacer sleeve, and the fuel resides on the burnish mark of the pressure tube. The bundle is then supported in a fashion which contributes to increased levels of vibration. Those pads which (due to geometric variation) have contact loads with the pressure tube within a certain range, vibrate, and cause significant fretting on the burnish mark, and further along at the midplane of the bundle. Inspection of the pressure tubes in Bruce A, Bruce B, and Darlington has revealed fret damage up to 0.55 mm at the burnish mark and slightly lower than this at the inlet bundle midplane. To date, all fret marks have been dealt with successfully without the need for tube replacement, but a program of work has been initiated to understand the mechanism and reduce the fretting. Such understanding is necessary to guide future design changes to the fuel bundle, to guide future inspection programs, to guide maintenance programs, and for longer term strategic planning. This paper discusses how the understanding of fretting has evolved and outlines a current hypothesis for the mechanism of fretting. The role of bundle geometry, excitation forces, and reactor conditions are reviewed, along with options under consideration to mitigate damage. (author). 4 refs., 2 tabs., 13 figs.

  12. Fuel bundle to pressure tube fretting in Bruce and Darlington

    International Nuclear Information System (INIS)

    Norsworthy, A.G.; Ditschun, A.

    1995-01-01

    As the fuel channel elongates due to creep, the fuel string moves relative to the inlet until the fuel pads at the inboard end eventually separate from the spacer sleeve, and the fuel resides on the burnish mark of the pressure tube. The bundle is then supported in a fashion which contributes to increased levels of vibration. Those pads which (due to geometric variation) have contact loads with the pressure tube within a certain range, vibrate, and cause significant fretting on the burnish mark, and further along at the midplane of the bundle. Inspection of the pressure tubes in Bruce A, Bruce B, and Darlington has revealed fret damage up to 0.55 mm at the burnish mark and slightly lower than this at the inlet bundle midplane. To date, all fret marks have been dealt with successfully without the need for tube replacement, but a program of work has been initiated to understand the mechanism and reduce the fretting. Such understanding is necessary to guide future design changes to the fuel bundle, to guide future inspection programs, to guide maintenance programs, and for longer term strategic planning. This paper discusses how the understanding of fretting has evolved and outlines a current hypothesis for the mechanism of fretting. The role of bundle geometry, excitation forces, and reactor conditions are reviewed, along with options under consideration to mitigate damage. (author). 4 refs., 2 tabs., 13 figs

  13. Standard test method for damage to contacting solid surfaces under fretting conditions

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2010-01-01

    1.1 This test method covers the studying or ranking the susceptibility of candidate materials to fretting corrosion or fretting wear for the purposes of material selection for applications where fretting corrosion or fretting wear can limit serviceability. 1.2 This test method uses a tribological bench test apparatus with a mechanism or device that will produce the necessary relative motion between a contacting hemispherical rider and a flat counterface. The rider is pressed against the flat counterface with a loading mass. The test method is intended for use in room temperature air, but future editions could include fretting in the presence of lubricants or other environments. 1.3 The purpose of this test method is to rub two solid surfaces together under controlled fretting conditions and to quantify the damage to both surfaces in units of volume loss for the test method. 1.4 The values stated in SI units are to be regarded as standard. No other units of measurement are included in this standard. 1.5...

  14. Wave propagation in coated cylinders with reference to fretting fatigue

    Indian Academy of Sciences (India)

    is to study stress wave propagation in cylinders with reference to high frequency fretting. ... The motivation for studying of fretting fatigue at higher frequency is to investigate the ... Hence focus in this work is given to thin rods and cylinders. The.

  15. Evaluation of surface characteristics under fretting of electrical contacts: Removal behaviour of hot dipped tin coating

    International Nuclear Information System (INIS)

    Park, Young Woo; Ramesh Bapu, G.N.K.; Lee, Kang Yong

    2009-01-01

    The fretting corrosion behaviour of hot dipped tin coating is investigated at low fretting cycles at ±25 μm displacement amplitude, 0.5N normal load, 3 Hz frequency, 45-50% relative humidity, and 25 ± 1 deg. C temperature. The typical characteristics of the change in contact resistance with fretting cycles are explained. The fretted surface is examined using laser scanning microscope, scanning electron microscope and energy dispersive X-ray analysis to assess the surface profile, extent of fretting damage, extent of oxidation and elemental distribution across the contact zone. The interdependence of extent of wear and oxidation increases the complexity of the fretting corrosion behaviour of tin coating. The variation of contact resistance clearly revealed the fretting of tin coating from 50 to 1200 cycles and the fretting of the substrate above 1200 cycles. The observed low and stable contact resistance region and the fluctuating resistance region at various fretting cycles are explained and substantiated with Scanning electron microscopy (SEM), laser scanning microscope (LSM) and energy dispersive analysis of X-rays (EDAX) analysis results of the fretted surface.

  16. Fluorescence Lifetime Readouts of Troponin-C-Based Calcium FRET Sensors: A Quantitative Comparison of CFP and mTFP1 as Donor Fluorophores

    Science.gov (United States)

    Laine, Romain; Stuckey, Daniel W.; Manning, Hugh; Warren, Sean C.; Kennedy, Gordon; Carling, David

    2012-01-01

    We have compared the performance of two Troponin-C-based calcium FRET sensors using fluorescence lifetime read-outs. The first sensor, TN-L15, consists of a Troponin-C fragment inserted between CFP and Citrine while the second sensor, called mTFP-TnC-Cit, was realized by replacing CFP in TN-L15 with monomeric Teal Fluorescent Protein (mTFP1). Using cytosol preparations of transiently transfected mammalian cells, we have measured the fluorescence decay profiles of these sensors at controlled concentrations of calcium using time-correlated single photon counting. These data were fitted to discrete exponential decay models using global analysis to determine the FRET efficiency, fraction of donor molecules undergoing FRET and calcium affinity of these sensors. We have also studied the decay profiles of the donor fluorescent proteins alone and determined the sensitivity of the donor lifetime to temperature and emission wavelength. Live-cell fluorescence lifetime imaging (FLIM) of HEK293T cells expressing each of these sensors was also undertaken. We confirmed that donor fluorescence of mTFP-TnC-Cit fits well to a two-component decay model, while the TN-L15 lifetime data was best fitted to a constrained four-component model, which was supported by phasor analysis of the measured lifetime data. If the constrained global fitting is employed, the TN-L15 sensor can provide a larger dynamic range of lifetime readout than the mTFP-TnC-Cit sensor but the CFP donor is significantly more sensitive to changes in temperature and emission wavelength compared to mTFP and, while the mTFP-TnC-Cit solution phase data broadly agreed with measurements in live cells, this was not the case for the TN-L15 sensor. Our titration experiment also indicates that a similar precision in determination of calcium concentration can be achieved with both FRET biosensors when fitting a single exponential donor fluorescence decay model to the fluorescence decay profiles. We therefore suggest that mTFP-based

  17. Turbulence induced Fretting-wear characteristics of steam generator helical tubes

    International Nuclear Information System (INIS)

    Jhung, Myung Jo; Jo, Jong Chull; Kim, Hho Jung; Yune, Young Gill; Yu, Seon Oh

    2005-01-01

    This study addresses safety assessment of the potential for fretting-wear damages on steam generator helical tubes due to turbulence-induced vibration in operating nuclear power plants. To get the natural frequency, corresponding mode shape and participation factor, modal analyses are performed for helical type tubes with various conditions. Special emphases are put on the effects of coil diameter and the number of turns on the modal and fretting wear characteristics of tubes. Also, investigated are the effects of external pressure on the tube modal characteristics as well as the effects of turbulence induced vibration on the fretting-wear characteristics of tubes

  18. Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization

    Science.gov (United States)

    Okamura, Yukio; Kondo, Satoshi; Sase, Ichiro; Suga, Takayuki; Mise, Kazuyuki; Furusawa, Iwao; Kawakami, Shigeki; Watanabe, Yuichiro

    2000-01-01

    A set of fluorescently-labeled DNA probes that hybridize with the target RNA and produce fluorescence resonance energy transfer (FRET) signals can be utilized for the detection of specific RNA. We have developed probe sets to detect and discriminate single-strand RNA molecules of plant viral genome, and sought a method to improve the FRET signals to handle in vivo applications. Consequently, we found that a double-labeled donor probe labeled with Bodipy dye yielded a remarkable increase in fluorescence intensity compared to a single-labeled donor probe used in an ordinary FRET. This double-labeled donor system can be easily applied to improve various FRET probes since the dependence upon sequence and label position in enhancement is not as strict. Furthermore this method could be applied to other nucleic acid substances, such as oligo RNA and phosphorothioate oligonucleotides (S-oligos) to enhance FRET signal. Although the double-labeled donor probes labeled with a variety of fluorophores had unexpected properties (strange UV-visible absorption spectra, decrease of intensity and decay of donor fluorescence) compared with single-labeled ones, they had no relation to FRET enhancement. This signal amplification mechanism cannot be explained simply based on our current results and knowledge of FRET. Yet it is possible to utilize this double-labeled donor system in various applications of FRET as a simple signal-enhancement method. PMID:11121494

  19. Fretting wear simulation of press-fitted shaft with finite element analysis and influence function method

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dong Hyong; Kwon, Seok Jin [Korea Railroad Research Institute, Uiwang (Korea, Republic of); Choi, Jae Boong; Kim, Young Jin [Sungkyunkwan University, Suwon (Korea, Republic of)

    2008-01-15

    In this paper the fretting wear of press-fitted specimens subjected to a cyclic bending load was simulated using finite element analysis and numerical method. The amount of microslip and contact variable at press-fitted and bending load condition in a press-fitted shaft was analysed by applying finite element method. With the finite element analysis result, a numerical approach was applied to predict fretting wear based on modified Archard's equation and updating the change of contact pressure caused by local wear with influence function method. The predicted wear profiles of press-fitted specimens at the contact edge wear compared with the experimental results obtained by rotating bending fatigue tests. It is shown that the depth of fretting wear by repeated slip between shaft and boss reaches the maximum value at the contact edge. The initial surface profile is continuously changed by the wear at the contact edge, and then the corresponding contact variables are redistributed. The work establishes a basis for numerical simulation of fretting wear on press fits.

  20. Fretting wear simulation of press-fitted shaft with finite element analysis and influence function method

    International Nuclear Information System (INIS)

    Lee, Dong Hyong; Kwon, Seok Jin; Choi, Jae Boong; Kim, Young Jin

    2008-01-01

    In this paper the fretting wear of press-fitted specimens subjected to a cyclic bending load was simulated using finite element analysis and numerical method. The amount of microslip and contact variable at press-fitted and bending load condition in a press-fitted shaft was analysed by applying finite element method. With the finite element analysis result, a numerical approach was applied to predict fretting wear based on modified Archard's equation and updating the change of contact pressure caused by local wear with influence function method. The predicted wear profiles of press-fitted specimens at the contact edge wear compared with the experimental results obtained by rotating bending fatigue tests. It is shown that the depth of fretting wear by repeated slip between shaft and boss reaches the maximum value at the contact edge. The initial surface profile is continuously changed by the wear at the contact edge, and then the corresponding contact variables are redistributed. The work establishes a basis for numerical simulation of fretting wear on press fits

  1. [Detection of protein-protein interactions by FRET and BRET methods].

    Science.gov (United States)

    Matoulková, E; Vojtěšek, B

    2014-01-01

    Nowadays, in vivo protein-protein interaction studies have become preferable detecting meth-ods that enable to show or specify (already known) protein interactions and discover their inhibitors. They also facilitate detection of protein conformational changes and discovery or specification of signaling pathways in living cells. One group of in vivo methods enabling these findings is based on fluorescent resonance energy transfer (FRET) and its bio-luminescent modification (BRET). They are based on visualization of protein-protein interactions via light or enzymatic excitation of fluorescent or bio-luminescent proteins. These methods allow not only protein localization within the cell or its organelles (or small animals) but they also allow us to quantify fluorescent signals and to discover weak or strong interaction partners. In this review, we explain the principles of FRET and BRET, their applications in the characterization of protein-protein interactions and we describe several findings using these two methods that clarify molecular and cellular mechanisms and signals related to cancer biology.

  2. Fretting fatigue behaviour of Ni-free high-nitrogen stainless steel in a simulated body fluid

    Directory of Open Access Journals (Sweden)

    Norio Maruyama, Sachiko Hiromoto, Eiji Akiyama and Morihiko Nakamura

    2013-01-01

    Full Text Available Fretting fatigue behaviour of Ni-free high-nitrogen steel (HNS with a yield strength of about 800 MPa, which was prepared by nitrogen gas pressurized electroslag remelting, was studied in air and in phosphate-buffered saline (PBS(-. For comparison, fretting fatigue behaviour of cold-rolled SUS316L steel (SUS316L(CR with similar yield strength was examined. The plain fatigue limit of HNS was slightly lower than that of SUS316L(CR although the former had a higher tensile strength than the latter. The fretting fatigue limit of HNS was higher than that of SUS316L(CR both in air and in PBS(-. A decrease in fatigue limit of HNS by fretting was significantly smaller than that of SUS316L(CR in both environments, indicating that HNS has better fretting fatigue resistance than SUS316L(CR. The decrease in fatigue limit by fretting is discussed taking into account the effect of friction stress due to fretting and the additional influences of wear, tribocorrosion and plastic deformation in the fretted area.

  3. Roughness Influence on Initiation of Fretting Fatigue Scar of Ti-6Al-4V Alloy

    Science.gov (United States)

    Capitanu, L.; Badita, L. L.; Florescu, V.; Tiganesteanu, C.

    2018-01-01

    This paper reports on the experimental studies undertaken to detect the early stage when appears the fretting wear of the Ti-6Al-4V alloy used for the hip prostheses. Wear is a critical aspect for estimating the fretting fatigue. Studies were performed on samples of special shape, in order to be able to study the influence of in contact surfaces roughness on the durability to fretting. Fretting buffers, with roughnesses Ra of the contact surface of 0.015 and 0.045 μm, and Ti-6Al-4V samples with roughnesses Ra = 0.045 μm, Ra = 0.075 μm and Ra = 0.19 μm, were used. Testing periods of 3 seconds, 1 minute and 5 minutes were selected to capture the moment of the fretting scar appearance, long before these initiate the eventual fretting cracking. Simultaneously with fretting wear of the surface, the friction coefficient was also measured. From the in time evolution determinations of the fretting wear, it resulted that, under the experimental conditions used, the minimum wear occurs at a certain value of the roughness and not at the minimum roughness. Surprisingly, the minimum friction coefficient does not coincide with the minimum fretting wear.

  4. Extraction of information on macromolecular interactions from fluorescence micro-spectroscopy measurements in the presence and absence of FRET

    Science.gov (United States)

    Raicu, Valerică

    2018-06-01

    Investigations of static or dynamic interactions between proteins or other biological macromolecules in living cells often rely on the use of fluorescent tags with two different colors in conjunction with adequate theoretical descriptions of Förster Resonance Energy Transfer (FRET) and molecular-level micro-spectroscopic technology. One such method based on these general principles is FRET spectrometry, which allows determination of the quaternary structure of biomolecules from cell-level images of the distributions, or spectra of occurrence frequency of FRET efficiencies. Subsequent refinements allowed combining FRET frequency spectra with molecular concentration information, thereby providing the proportion of molecular complexes with various quaternary structures as well as their binding/dissociation energies. In this paper, we build on the mathematical principles underlying FRET spectrometry to propose two new spectrometric methods, which have distinct advantages compared to other methods. One of these methods relies on statistical analysis of color mixing in subpopulations of fluorescently tagged molecules to probe molecular association stoichiometry, while the other exploits the color shift induced by FRET to also derive geometric information in addition to stoichiometry. The appeal of the first method stems from its sheer simplicity, while the strength of the second consists in its ability to provide structural information.

  5. Characterizing single-molecule FRET dynamics with probability distribution analysis.

    Science.gov (United States)

    Santoso, Yusdi; Torella, Joseph P; Kapanidis, Achillefs N

    2010-07-12

    Probability distribution analysis (PDA) is a recently developed statistical tool for predicting the shapes of single-molecule fluorescence resonance energy transfer (smFRET) histograms, which allows the identification of single or multiple static molecular species within a single histogram. We used a generalized PDA method to predict the shapes of FRET histograms for molecules interconverting dynamically between multiple states. This method is tested on a series of model systems, including both static DNA fragments and dynamic DNA hairpins. By fitting the shape of this expected distribution to experimental data, the timescale of hairpin conformational fluctuations can be recovered, in good agreement with earlier published results obtained using different techniques. This method is also applied to studying the conformational fluctuations in the unliganded Klenow fragment (KF) of Escherichia coli DNA polymerase I, which allows both confirmation of the consistency of a simple, two-state kinetic model with the observed smFRET distribution of unliganded KF and extraction of a millisecond fluctuation timescale, in good agreement with rates reported elsewhere. We expect this method to be useful in extracting rates from processes exhibiting dynamic FRET, and in hypothesis-testing models of conformational dynamics against experimental data.

  6. Fluorescence lifetime FRET imaging of receptor-ligand complexes in tumor cells in vitro and in vivo

    Science.gov (United States)

    Rudkouskaya, Alena; Sinsuebphon, Nattawut; Intes, Xavier; Mazurkiewicz, Joseph E.; Barroso, Margarida

    2017-02-01

    To guide the development of targeted therapies with improved efficacy and accelerated clinical acceptance, novel imaging methodologies need to be established. Toward this goal, fluorescence lifetime Förster resonance energy transfer (FLIM-FRET) imaging assays capitalize on the ability of antibodies or protein ligands to bind dimerized membrane bound receptors to measure their target engagement levels in cancer cells. Conventional FLIM FRET microscopy has been widely applied at visible wavelengths to detect protein-protein interactions in vitro. However, operation at these wavelengths restricts imaging quality and ability to quantitate lifetime changes in in vivo small animal optical imaging due to high auto-fluorescence and light scattering. Here, we have analyzed the uptake of iron-bound transferrin (Tf) probes into human breast cancer cells using FLIM-FRET microscopy in the visible and near-infrared (NIR) range. The development of NIR FLIM FRET microscopy allows for the use of quantitative lifetime-based molecular assays to measure drug-target engagement levels at multiple scales: from in vitro microscopy to in vivo small animal optical imaging (macroscopy). This novel approach can be extended to other receptors, currently targeted in oncology. Hence, lifetime-based molecular imaging can find numerous applications in drug delivery and targeted therapy assessment and optimization.

  7. Förster Resonance Energy Transfer (FRET) from Triton X-100 to 4-benzothiazol-2-yl-phenol: Varying FRET efficiency with CMC of the donor (Triton X-100)

    International Nuclear Information System (INIS)

    Paul, Bijan Kumar; Ganguly, Aniruddha; Karmakar, Saswati; Guchhait, Nikhil

    2013-01-01

    A heterocyclic compound viz., 4-benzothiazol-2-yl-phenol (4B2YP) has been synthesized and its photophysics have been examined through steady-state absorption, emission and time resolved emission spectroscopic techniques, in brief. Then 4B2YP has been exploited as an acceptor in the Förster Resonance Energy Transfer (FRET) process from photoexcited benzene aromatic nucleus of Triton X-100 (TX-100) surfactant. Dependence of the energy transfer efficiency on the donor concentration with respect to its critical micelle concentration (CMC) is clearly reflected in the study. High values of Stern–Volmer constant (K SV ) for quenching of the donor fluorescence in the presence of the acceptor suggest the operation of long-range dipole–dipole interaction in the course of energy transfer process, while the inference is aptly supported from time resolved fluorescence decay results. Experimental results show maximum FRET efficiency at the CMC of the donor (TX-100). -- Highlights: • FRET from neutral surfactant Triton X-100 to chromophore 4-benzothiazol-2-yl-phenol. • Steady state and time resolved spectroscopy. • Long-range dipole–dipole interaction responsible for FRET. • FRET efficiency as a measure of CMC of surfactant

  8. Förster Resonance Energy Transfer (FRET) from Triton X-100 to 4-benzothiazol-2-yl-phenol: Varying FRET efficiency with CMC of the donor (Triton X-100)

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Bijan Kumar, E-mail: bijan.paul.chem.cu@gmail.com [Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009 (India); Ganguly, Aniruddha [Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009 (India); Karmakar, Saswati [Department of Chemistry, Sree Chaitanya College, Habra, North 24 Parganas (India); Guchhait, Nikhil, E-mail: nguchhait@yahoo.com [Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009 (India)

    2013-11-15

    A heterocyclic compound viz., 4-benzothiazol-2-yl-phenol (4B2YP) has been synthesized and its photophysics have been examined through steady-state absorption, emission and time resolved emission spectroscopic techniques, in brief. Then 4B2YP has been exploited as an acceptor in the Förster Resonance Energy Transfer (FRET) process from photoexcited benzene aromatic nucleus of Triton X-100 (TX-100) surfactant. Dependence of the energy transfer efficiency on the donor concentration with respect to its critical micelle concentration (CMC) is clearly reflected in the study. High values of Stern–Volmer constant (K{sub SV}) for quenching of the donor fluorescence in the presence of the acceptor suggest the operation of long-range dipole–dipole interaction in the course of energy transfer process, while the inference is aptly supported from time resolved fluorescence decay results. Experimental results show maximum FRET efficiency at the CMC of the donor (TX-100). -- Highlights: • FRET from neutral surfactant Triton X-100 to chromophore 4-benzothiazol-2-yl-phenol. • Steady state and time resolved spectroscopy. • Long-range dipole–dipole interaction responsible for FRET. • FRET efficiency as a measure of CMC of surfactant.

  9. FRET-based localization of fluorescent protein insertions within the ryanodine receptor type 1.

    Directory of Open Access Journals (Sweden)

    Shweta A Raina

    Full Text Available Fluorescent protein (FP insertions have often been used to localize primary structure elements in mid-resolution 3D cryo electron microscopic (EM maps of large protein complexes. However, little is known as to the precise spatial relationship between the location of the fused FP and its insertion site within a larger protein. To gain insights into these structural considerations, Förster resonance energy transfer (FRET measurements were used to localize green fluorescent protein (GFP insertions within the ryanodine receptor type 1 (RyR1, a large intracellular Ca(2+ release channel that plays a key role in skeletal muscle excitation contraction coupling. A series of full-length His-tagged GFP-RyR1 fusion constructs were created, expressed in human embryonic kidney (HEK-293T cells and then complexed with Cy3NTA, a His-tag specific FRET acceptor. FRET efficiency values measured from each GFP donor to Cy3NTA bound to each His tag acceptor site were converted into intermolecular distances and the positions of each inserted GFP were then triangulated relative to a previously published X-ray crystal structure of a 559 amino acid RyR1 fragment. We observed that the chromophoric centers of fluorescent proteins inserted into RyR1 can be located as far as 45 Å from their insertion sites and that the fused proteins can also be located in internal cavities within RyR1. These findings should prove useful in interpreting structural results obtained in cryo EM maps using fusions of small fluorescent proteins. More accurate point-to-point distance information may be obtained using complementary orthogonal labeling systems that rely on fluorescent probes that bind directly to amino acid side chains.

  10. Investigation of fretting behaviour in pressure armour layers of flexible pipes

    Science.gov (United States)

    Don Rasika Perera, Solangarachchige

    The incidence of fretting damage in the pressure armour wires of flexible pipes used in offshore oil explorations has been investigated. A novel experimental facility which is capable of simulating nub and valley contact conditions of interlocking wire winding with dynamic slip, representative of actual pipe loading, has been developed. The test set-up is equipped with a state of the art data acquisition system and a controller with transducers to measure and control the normal load, slip amplitude and friction force at the contact, in addition to the hoop stress in the wire. Tests were performed with selected loading and the fretted regions were examined using optical microscopy techniques. Results show that the magnitude of contact loading and the slip amplitude have a distinct influence on surface damage. Surface cracks originated from a fretting scar were observed at high contact loads in mixed slip sliding while surface damage predominantly due to wear was observed under gross slip. The position of surface cracks and the wear profile have been related to the contact pressure distribution. The evolution of friction force and surface damage under different slip and normal pressure conditions has been analysed. A fracture mechanics based numerical procedure has been developed to analyse the fretting damage behaviour. A severity parameter is proposed in order to ascertain whether the crack growth is in mode I or mode II cracking. The analysis show the influence of mode II cracking in the early stages of crack growth following which the crack deviates in the mode I direction making mode I the dominant crack propagation mechanism. The crack path determined by the numerical procedure correlates well with the experimental results. A numerical analysis was carried out for the fretting fatigue condition where a cyclic bulk stress superimposes with the friction force. The analysis correlates well with short crack growth behaviour. The analysis confirms that fretting is a

  11. Effects of fretting fatigue on the residual stress of shot peened Ti-6Al-4V samples

    International Nuclear Information System (INIS)

    Martinez, S.A.; Sathish, S.; Blodgett, M.P.; Mall, S.; Namjoshi, S.

    2005-01-01

    X-ray diffraction residual stress measurement has been utilized as nondestructive tool for the characterization of fretting fatigue damage in shot peened samples of Ti-6Al-4V. Prior to fretting fatigue damage, compressive residual stresses were found to be uniform over the entire face of the sample and independent of the measurement direction. After fretting fatigue, inside and in the vicinity of the fretting damage zone large relaxation of compressive residual stress was observed. An anisotropic residual stress distribution has been observed in the fretting fatigue damaged region. Residual stress measurements in interrupted fretting fatigue experiments showed that the relaxation of residual stress increases as the number of fretting fatigue cycles increase. The results are discussed in the light of their importance in establishing X-ray diffraction residual stress measurement technique as a nondestructive tool to characterize fretting fatigue damage

  12. Radical-pair based avian magnetoreception

    Science.gov (United States)

    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.

  13. Fuel-element vibration and bearing pad to pressure tube fretting

    International Nuclear Information System (INIS)

    Fisher, N.J.; Taylor, C.E.; Pettigrew, M.J.

    1990-08-01

    Fuel channel operation under boiling condition results in increased flow velocities, which may lead to unacceptable fuel-element vibration and bearing pad to pressure tube fretting. The existing endurance test database does not fully cover the range of future channel operating conditions. In particular, after refuelling, some channels for future designs may operate with two-phase flow conditions outside the range of endurance test conditions. Full-scale endurance testing at realistic steam-water conditions involves substantial energy costs. Therefore, fundamental laboratory investigations were conducted to define and endurance test matrix which adequately envelops the future range of operating conditions while minimizing both the number of tests and the energy requirement of individual tests. The main focus of the laboratory investigations was to establish the relationships between: fuel channel flow conditions and fuel-element vibration; and fuel-element vibration and bearing pad to pressure tube fretting. The vibration response of a single fuel element was measured over a wide range of operating conditions covering realistic fuel channel conditions and simulated endurance testing conditions. For higher void fractions, the vibration amplitudes measured in air/water were much higher than in steam/water, while for low void fractions, the amplitudes were similar. The measured amplitudes in steam/water varied very little over the range of temperature and pressure investigated. The effects of temperature, pressure tube oxide thickness, vibration amplitude and bearing pad manufacturer on pressure tube fretting were investigated. The fretting rate is extremely temperature dependent. For vibration amplitudes about three or four times greater than expected in-reactor conditions, peak fretting rates were observed in the 225 to 286 degrees C temperature range. Fretting rates were seven times less at the higher temperatures of 300 and 315 degrees C, and the lower temperatures

  14. Application of FRET probes in the analysis of neuronal plasticity

    Directory of Open Access Journals (Sweden)

    Yoshibumi eUeda

    2013-10-01

    Full Text Available Breakthroughs in imaging techniques and optical probes in recent years have revolutionized the field of life sciences in ways that traditional methods could never match. The spatial and temporal regulation of molecular events can now be studied with great precision. There have been several key discoveries that have made this possible. Since GFP was cloned in 1992, it has become the dominant tracer of proteins in living cells. Then the evolution of color variants of GFP opened the door to the application of Förster resonance energy transfer (FRET, which is now widely recognized as a powerful tool to study complicated signal transduction events and interactions between molecules. Employment of fluorescent lifetime imaging microscopy (FLIM allows the precise detection of FRET in small subcellular structures such as dendritic spines. In this review, we provide an overview of the basic and practical aspects of FRET imaging and discuss how different FRET probes have revealed insights into the molecular mechanisms of synaptic plasticity and enabled visualization of neuronal network activity both in vitro and in vivo.

  15. Influence of plasma molybdenizing and shot-peening on fretting damage behavior of titanium alloy

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Chang-bin, E-mail: tcbtop@126.com [School of Metallurgy and Engineering, Xi’an University of Architecture and Technology, Xi’an, Shaanxi 710055 (China); Institute of Corrosion and Protection, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China); Liu, Dao-xin, E-mail: liudaox@nwpu.edu.cn [Institute of Corrosion and Protection, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China); Tang, Bin [Institute of Surface Engineering, Taiyuan University of Technology, Taiyuan Shanxi 030024 (China); Zhang, Xiao-hua [Institute of Corrosion and Protection, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China); Qin, Lin [Institute of Surface Engineering, Taiyuan University of Technology, Taiyuan Shanxi 030024 (China); Liu, Cheng-song [Institute of Corrosion and Protection, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 (China)

    2016-12-30

    Highlights: • Plasma molybdenizing increases FW resistance of Ti6Al4V, but reduces its FF life. • Shot-peened plasmamolybdenizing surface enhances FW and FF resistance of Ti6Al4V. • Combined treatment yields low surface-roughness & high hardness gradient distribution. • Combined treatment yields beneficial residual compressive stress & good toughness. • Anti-wear & -fatigue performance improvements for surface engineering applications. - Abstract: Effect of plasma molybdenizing and shot-peening on fretting wear and fretting fatigue behaviors of Ti6Al4V alloy was investigated. The plasma molybdenized layer composed of a dense molybdenum deposition layer and a Mo–Ti solid–solution layer can increase surface hardness by 2.8 times and cause its volume loss by fretting wear to decrease to 1/14 compared with that of the substrate. Plasma molybdenized treatment results in a significant decrease in resistance of the substrate to fretting fatigue. It is ascribed that the molybdenized layer with high hardness yields a low toughness, and its high surface roughness leads to a micro-notched effect. However, proper combination plasma molybdenizing and subsequent shot-peening may enhance the simultaneous fretting fatigue and fretting wear resistance of Ti6Al4V significantly, which can decrease the fretting wear volume loss to 1/27, and may increase the fretting fatigue life by more than 69 times. A synergistic improvement in fretting fatigue of the titanium alloy by combining surface alloying with shot-peening can be achieved. The results indicate that a beneficial residual compressive stress distribution, high surface hardness with suitable hardness gradient distribution, good apparent toughness, relatively low surface roughness, and excellent surface integrity are achieved.

  16. Electroporation and microinjection successfully deliver single-stranded and duplex DNA into live cells as detected by FRET measurements.

    Directory of Open Access Journals (Sweden)

    Rosemary A Bamford

    Full Text Available Förster resonance energy transfer (FRET technology relies on the close proximity of two compatible fluorophores for energy transfer. Tagged (Cy3 and Cy5 complementary DNA strands forming a stable duplex and a doubly-tagged single strand were shown to demonstrate FRET outside of a cellular environment. FRET was also observed after transfecting these DNA strands into fixed and live cells using methods such as microinjection and electroporation, but not when using lipid based transfection reagents, unless in the presence of the endosomal acidification inhibitor bafilomycin. Avoiding the endocytosis pathway is essential for efficient delivery of intact DNA probes into cells.

  17. Polyfluorophore Excimers and Exciplexes as FRET Donors in DNA

    Science.gov (United States)

    Teo, Yin Nah; Kool, Eric T.

    2009-01-01

    We describe studies aimed at testing whether oligomeric exciplex- and excimer fluorophores conjugated to DNA have the potential to act as donors for energy transfer by the Förster mechanism. Oligodeoxyfluorosides (ODFs) are composed of stacked, electronically interacting fluorophores replacing the bases on a DNA scaffold. The monomer chromophores in the twenty tetramer-length ODFs studied here include pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and a nonfluorescent spacer (S); these are conjugated in varied combinations at the 3’ end of a 14mer DNA probe sequence. In the absence of an acceptor chromophore, many of the ODF-DNAs show broad, unstructured long-wavelength emission peaks characteristic of excimer and exciplex excited states, similar to what has been observed for unconjugated ODFs. Although such delocalized excited states have been widely studied, we know of no prior report of their use in FRET. We tested the ability of the twenty ODFs to donate energy to Cy5 and TAMRA dyes conjugated to a complementary strand of DNA, with these acceptors oriented either at the near or far end of the ODF-conjugated probes. Results showed that a number of the ODF fluorophores exhibited relatively efficient energy transfer characteristic of the Förster mechanism, as judged by drops in donor emission quantum yield and fluorescence lifetime, accompanied by increases in intensity of acceptor emission bands. Excimer/exciplex bands in the donors were selectively quenched while shorter-wavelength monomer emission stayed relatively constant, consistent with the notion that the delocalized excited states, rather than individual fluorophores, are the donors. Interestingly, only specific sequences of ODFs were able to act as donors, while others did not, even though their emission wavelengths were similar. The new FRET donors possess large Stokes shifts, which can be beneficial for multiple applications. In addition, all ODFs can be excited at a single

  18. Fretting and wear of stainless and ferritic steels in LMFBR steam generators

    International Nuclear Information System (INIS)

    Lewis, M.W.J.; Campbell, C.S.

    1981-01-01

    Steam generators for LMFBR's may be subject to both fretting wear as a result of flow-induced vibrations and to wear from larger amplitude sliding movements from thermal changes. Results of tests simulating the latter are given for stainless and ferritic steels. For the assessment of fretting wear damage, vibration assessments must be combined with data on specific wear rates. Test mechanisms used to study fretting in sodium covering impact, impact-slide and pure rubbing are described and results presented. (author)

  19. MIL-L-87177 and CLT:X-10 Lubricants Improve Electrical Connector Fretting Corrosion Behavior

    International Nuclear Information System (INIS)

    AUKLAND, NEIL R.; HANLON, JAMES T.

    1999-01-01

    We have conducted a fretting research project using MIL-L-87177 and CLT: X-10 lubricants on Nano-miniature connectors. When they were fretted without lubricant, individual connectors first exceeded our 0.5 ohm failure criteria from 2,341 to 45,238 fretting cycles. With additional fretting, their contact resistance increased to more than 100,000 ohms. Unmodified MIL-L-87177 lubricant delayed the onset of first failure to between 430,000 and over 20,000,000 fretting cycles. MIL-L-87177 modified by addition of Teflon powder delayed first failure to beyond 5 million fretting cycles. Best results were obtained when Teflon was used and also when both the straight and modified lubricants were poured into and then out of the connector. CLT: X-10 lubricant delayed the onset of first failure to beyond 55 million cycles in one test where a failure was actually observed and to beyond 20 million cycles in another that was terminated without failure. CLT: X-10 recovered an unlubricated connector driven deeply into failure, with six failed pins recovering immediately and four more recovering during an additional 420 thousand fretting cycles. MIL-L-87177 was not able to recover a connector under similar conditions

  20. Towards understanding the E. coli PNP binding mechanism and FRET absence between E. coli PNP and formycin A.

    Science.gov (United States)

    Prokopowicz, Małgorzata; Greń, Bartosz; Cieśla, Joanna; Kierdaszuk, Borys

    2017-11-01

    The aim of this study is threefold: (1) augmentation of the knowledge of the E. coli PNP binding mechanism; (2) explanation of the previously observed 'lack of FRET' phenomenon and (3) an introduction of the correction (modified method) for FRET efficiency calculation in the PNP-FA complexes. We present fluorescence studies of the two E. coli PNP mutants (F159Y and F159A) with formycin A (FA), that indicate that the aromatic amino acid is indispensable in the nucleotide binding, additional hydroxyl group at position 159 probably enhances the strength of binding and that the amino acids pair 159-160 has a great impact on the spectroscopic properties of the enzyme. The experiments were carried out in hepes and phosphate buffers, at pH7 and 8.3. Two methods, a conventional and a modified one, that utilizes the dissociation constant, for calculations of the energy transfer efficiency (E) and the acceptor-to-donor distance (r) between FA and the Tyr (energy donor) were employed. Total difference spectra were calculated for emission spectra (λ ex 280nm, 295nm, 305nm and 313nm) for all studied systems. Time-resolved techniques allowed to conclude the existence of a specific structure formed by amino acids at positions 159 and 160. The results showed an unexpected pattern change of FRET in the mutants, when compared to the wild type enzyme and a probable presence of a structure created between 159 and 160 residue, that might influence the binding efficiency. Additionally, we confirmed the indispensable role of the modification of the FRET efficiency (E) calculation on the fraction of enzyme saturation in PNP-FA systems. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Spin contamination analogy, Kramers pairs symmetry and spin density representations at the 2-component unrestricted Hartree-Fock level of theory

    KAUST Repository

    Bučinský, Lukáš

    2015-05-11

    "Kramers pairs symmetry breaking" is evaluated at the 2-component (2c) Kramers unrestricted and/or general complex Hartree-Fock (GCHF) level of theory, and its analogy with "spin contamination" at the 1-component (1c) unrestricted Hartree-Fock (UHF) level of theory is emphasized. The GCHF "Kramers pairs symmetry breaking" evaluation is using the square of overlaps between the set of occupied spinorbitals with the projected set of Kramers pairs. In the same fashion, overlaps between α and β orbitals are used in the evaluation of "spin contamination" at the UHF level of theory. In this manner, UHF Š2 expectation value is made formally extended to the GCHF case. The directly evaluated GCHF expectation value of the Š2 operator is considered for completeness. It is found that the 2c GCHF Kramers pairs symmetry breaking has a very similar extent in comparison to the 1c UHF spin contamination. Thus higher excited states contributions to the 1c and 2c unrestricted wave functions of open shell systems have almost the same extent and physical consequences. Moreover, it is formally shown that a single determinant wave function in the restricted open shell Kramers case has the expectation value of K2 operator equal to the negative number of open shell electrons, while the eigenvalue of K2 for the series of simple systems (H, He, He*-triplet, Li and Li*-quartet) are found to be equal to minus the square of the number of open shell electrons. The concept of unpaired electron density is extended to the GCHF regime and compared to UHF and restricted open shell Hartree-Fock spin density. The "collinear" and "noncollinear" analogs of spin density at the GCHF level of theory are considered as well. Spin contamination and/or Kramers pairs symmetry breaking, spin populations and spin densities are considered for H2O+, Cl, HCl+, phenoxyl radical (C6H5O) as well as for Cu, Cu2+, Fe and the [OsCl5(1H-pyrazole)]- anion. The 1c and 2c unpaired electron density representation is found

  2. Preliminary Study on the Fretting Wear Behaviors of a Duel Cooled Fuel Rod

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.H.; Lee, K.H.; Kim, H.K. [KAERI, 150 Dukjin-dong Yuseon-gu Daejeon, 305-353 (Korea, Republic of)

    2009-06-15

    Based on MIT's concept, an innovative fuel development project was launched by KAERI that a substantial power up-rating could be realized by introducing an internally and externally double cooled annular fuel for current PWR reactors. In order to apply this duel cooled fuel to an OPR 1000 reactor system, geometrical features of structural parts in a fuel assembly should be changed except an overall dimension of a fuel assembly. Typical changes are summarized as fuel rod diameter and weight, shape and position of a spacer grid spring, etc. When considering a duel cooled fuel rod, its vibration characteristic and fretting behavior should be verified because the modified shape and dimension of spacer grid spring, fuel rod diameter and weight, number of spacer grid assembly are closely related to a flow-induced vibration in a duel cooled fuel assembly. In this study, based on FIV test results of 4x4 fuel assembly, fretting wear tests of an outer duel cooled fuel rod were performed by using an embossing type spacer grid spring that could adjust its spring stiffness. The discussion was focused on the evaluation of the optimized spring stiffness and spring position in 1x1 cell by analyzing the fretting wear results. (authors)

  3. DNA base pair resolution measurements using resonance energy transfer efficiency in lanthanide doped nanoparticles.

    Directory of Open Access Journals (Sweden)

    Aleksandra Delplanque

    Full Text Available Lanthanide-doped nanoparticles are of considerable interest for biodetection and bioimaging techniques thanks to their unique chemical and optical properties. As a sensitive luminescence material, they can be used as (bio probes in Förster Resonance Energy Transfer (FRET where trivalent lanthanide ions (La3+ act as energy donors. In this paper we present an efficient method to transfer ultrasmall (ca. 8 nm NaYF4 nanoparticles dispersed in organic solvent to an aqueous solution via oxidation of the oleic acid ligand. Nanoparticles were then functionalized with single strand DNA oligomers (ssDNA by inducing covalent bonds between surface carboxylic groups and a 5' amine modified-ssDNA. Hybridization with the 5' fluorophore (Cy5 modified complementary ssDNA strand demonstrated the specificity of binding and allowed the fine control over the distance between Eu3+ ions doped nanoparticle and the fluorophore by varying the number of the dsDNA base pairs. First, our results confirmed nonradiative resonance energy transfer and demonstrate the dependence of its efficiency on the distance between the donor (Eu3+ and the acceptor (Cy5 with sensitivity at a nanometre scale.

  4. DNA base pair resolution measurements using resonance energy transfer efficiency in lanthanide doped nanoparticles.

    Science.gov (United States)

    Delplanque, Aleksandra; Wawrzynczyk, Dominika; Jaworski, Pawel; Matczyszyn, Katarzyna; Pawlik, Krzysztof; Buckle, Malcolm; Nyk, Marcin; Nogues, Claude; Samoc, Marek

    2015-01-01

    Lanthanide-doped nanoparticles are of considerable interest for biodetection and bioimaging techniques thanks to their unique chemical and optical properties. As a sensitive luminescence material, they can be used as (bio) probes in Förster Resonance Energy Transfer (FRET) where trivalent lanthanide ions (La3+) act as energy donors. In this paper we present an efficient method to transfer ultrasmall (ca. 8 nm) NaYF4 nanoparticles dispersed in organic solvent to an aqueous solution via oxidation of the oleic acid ligand. Nanoparticles were then functionalized with single strand DNA oligomers (ssDNA) by inducing covalent bonds between surface carboxylic groups and a 5' amine modified-ssDNA. Hybridization with the 5' fluorophore (Cy5) modified complementary ssDNA strand demonstrated the specificity of binding and allowed the fine control over the distance between Eu3+ ions doped nanoparticle and the fluorophore by varying the number of the dsDNA base pairs. First, our results confirmed nonradiative resonance energy transfer and demonstrate the dependence of its efficiency on the distance between the donor (Eu3+) and the acceptor (Cy5) with sensitivity at a nanometre scale.

  5. Inferring properties of disordered chains from FRET transfer efficiencies

    Science.gov (United States)

    Zheng, Wenwei; Zerze, Gül H.; Borgia, Alessandro; Mittal, Jeetain; Schuler, Benjamin; Best, Robert B.

    2018-03-01

    Förster resonance energy transfer (FRET) is a powerful tool for elucidating both structural and dynamic properties of unfolded or disordered biomolecules, especially in single-molecule experiments. However, the key observables, namely, the mean transfer efficiency and fluorescence lifetimes of the donor and acceptor chromophores, are averaged over a broad distribution of donor-acceptor distances. The inferred average properties of the ensemble therefore depend on the form of the model distribution chosen to describe the distance, as has been widely recognized. In addition, while the distribution for one type of polymer model may be appropriate for a chain under a given set of physico-chemical conditions, it may not be suitable for the same chain in a different environment so that even an apparently consistent application of the same model over all conditions may distort the apparent changes in chain dimensions with variation of temperature or solution composition. Here, we present an alternative and straightforward approach to determining ensemble properties from FRET data, in which the polymer scaling exponent is allowed to vary with solution conditions. In its simplest form, it requires either the mean FRET efficiency or fluorescence lifetime information. In order to test the accuracy of the method, we have utilized both synthetic FRET data from implicit and explicit solvent simulations for 30 different protein sequences, and experimental single-molecule FRET data for an intrinsically disordered and a denatured protein. In all cases, we find that the inferred radii of gyration are within 10% of the true values, thus providing higher accuracy than simpler polymer models. In addition, the scaling exponents obtained by our procedure are in good agreement with those determined directly from the molecular ensemble. Our approach can in principle be generalized to treating other ensemble-averaged functions of intramolecular distances from experimental data.

  6. Critical Shell Thickness of Core/Shell Upconversion Luminescence Nanoplatform for FRET Application

    NARCIS (Netherlands)

    Wang, Yu; Liu, Kai; Liu, Xiaomin; Dohnalova, Katerina; Gregorkiewicz, Tom; Kong, Xianggui; Aalders, Maurice C. G.; Buma, Wybren J.; Zhang, Hong

    2011-01-01

    Almost all the luminescence upconversion nanoparticles used for Forster resonant energy transfer (FRET) applications are bare cores based on the consideration that the energy transfer efficiency is optimized because the distance between energy donors and acceptors is minimized. On the other hand, it

  7. Impact Fretting Wear Behavior of Alloy 690 Tubes in Dry and Deionized Water Conditions

    Institute of Scientific and Technical Information of China (English)

    Zhen-Bing Cai; Jin-Fang Peng; Hao Qian; Li-Chen Tang; Min-Hao Zhu

    2017-01-01

    The impact fretting wear has largely occurred at nuclear power device induced by the flow-induced vibration,and it will take potential hazards to the service of the equipment.However,the present study focuses on the tangential fretting wear of alloy 690 tubes.Research on impact fretting wear of alloy 690 tubes is limited and the related research is imminent.Therefore,impact fretting wear behavior of alloy 690 tubes against 304 stainless steels is investigated.Deionized water is used to simulate the flow environment of the equipment,and the dry environment is used for comparison.Varied analytical techniques are employed to characterize the wear and tribochemical behavior during impact fretting wear.Characterization results indicate that cracks occur at high impact load in both water and dry equipment;however,the water as a medium can significantly delay the cracking time.The crack propagation behavior shows a jagged shape in the water,but crack extended disorderly in dry equipment because the water changed the stress distribution and retarded the friction heat during the wear process.The SEM and XPS analysis shows that the main failure mechanisms of the tube under impact fretting are fatigue wear and friction oxidation.The effect of medium(water) on fretting wear is revealed,which plays a potential and promising role in the service of nuclear power device and other flow equipments.

  8. Influence of Fretting on Flexural Fatigue of 304 Stainless Steel and Mild Steel

    National Research Council Canada - National Science Library

    Bill, Robert

    1978-01-01

    Fretting fatigue experiments conducted on 304 stainless steel using a flexural-fatigue test arrangement with bolted-on fretting pads have demonstrated that fatigue life is reduced by at least a factor...

  9. A New FRET-Based Sensitive DNA Sensor for Medical Diagnostics using PNA Probe and Water-Soluble Blue Light Emitting Polymer

    Directory of Open Access Journals (Sweden)

    Nidhi Mathur

    2008-01-01

    Full Text Available A reliable, fast, and low-cost biosensor for medical diagnostics using DNA sequence detection has been developed and tested for the detection of the bacterium “Bacillus anthracis.” In this sensor, Poly [9,9-di (6,6′- N, N′ trimethylammonium hexylfluorenyl-2, 7-diyl-alt-co- (1,4-phenylene] dibromide salt (PFP has been taken as cationic conjugated polymer (CCP and PNA attached with fluorescein dye (PNAC∗ as a probe. The basic principle of this sensor is that when a PNAC∗ probe is hybridized with a single strand DNA (ssDNA having complementary sequence, Forster resonance energy transfer (FRET may take place from PFP to the PNAC∗/DNA complex. If the FRET is efficient, the photoluminescence from the PFP will be highly quenched and that from PNAC∗ will be enhanced. On the other hand, if the DNA sequence is noncomplementary to PNA, FRET will not occur.

  10. Characteristics of CANDU fuel bundles that caused pressure tube fretting at the bundle midplane

    Energy Technology Data Exchange (ETDEWEB)

    Dennier, D; Manzer, A M [Atomic Energy of Canada Ltd., Mississauga, ON (Canada); Koehn, E [Ontario Hydro, Toronto, ON (Canada)

    1996-12-31

    Detailed measurements on new bundles, and those that caused fretting during in- and out-reactor tests, have given insight into the factors responsible for fretting at the midplane of the inlet bundle. Bottom fuel elements that were attached near radial endplate spokes and had inboard bearing pads in the rolled joint cavity produced a significant portion of the observed fret marks. These elements are influenced by several driving forces that deflect the centre bearing pads towards the pressure tube surface. The evidence suggests that slight changes in bundle design may be possible to reduce pressure tube fretting. (author). 4 refs., 3 tabs., 8 figs.

  11. RANKING RELATIONS USING ANALOGIES IN BIOLOGICAL AND INFORMATION NETWORKS1

    Science.gov (United States)

    Silva, Ricardo; Heller, Katherine; Ghahramani, Zoubin; Airoldi, Edoardo M.

    2013-01-01

    Analogical reasoning depends fundamentally on the ability to learn and generalize about relations between objects. We develop an approach to relational learning which, given a set of pairs of objects S = {A(1) : B(1), A(2) : B(2), …, A(N) : B(N)}, measures how well other pairs A : B fit in with the set S. Our work addresses the following question: is the relation between objects A and B analogous to those relations found in S? Such questions are particularly relevant in information retrieval, where an investigator might want to search for analogous pairs of objects that match the query set of interest. There are many ways in which objects can be related, making the task of measuring analogies very challenging. Our approach combines a similarity measure on function spaces with Bayesian analysis to produce a ranking. It requires data containing features of the objects of interest and a link matrix specifying which relationships exist; no further attributes of such relationships are necessary. We illustrate the potential of our method on text analysis and information networks. An application on discovering functional interactions between pairs of proteins is discussed in detail, where we show that our approach can work in practice even if a small set of protein pairs is provided. PMID:24587838

  12. Derivation of Elastic Stress Concentration Factor Equations for Debris Fretting Flaws in Pressure Tubes of Pressurized Heavy Water Reactors

    International Nuclear Information System (INIS)

    Kim, Jong Sung; Oh, Young Jin

    2014-01-01

    If volumetric flaws such as bearing pad fretting flaws and debris fretting flaws are detected in the pressure tubes of pressurized heavy water reactors during in-service inspection, the initiation of fatigue cracks and delayed hydrogen cracking from the detected volumetric flaws shall be assessed by using elastic stress concentration factors in accordance with CSA N285.8-05. The CSA N285.8-05 presents only an approximate formula based on linear elastic fracture mechanics for the debris fretting flaw. In this study, an engineering formula considering the geometric characteristics of the debris fretting flaw in detail was derived using two-dimensional finite element analysis and Kinectrics, Inc.'s engineering procedure with slight modifications. Comparing the application results obtained using the derived formula with the three-dimensional finite element analysis results, it is found that the results obtained using the derived formula agree well with the results of the finite element analysis

  13. Experimental facility design for study of fretting in steam generator tubes

    International Nuclear Information System (INIS)

    Balbiani, J.P.; Bergant, M.; Yawny, A.

    2012-01-01

    The design of an experimental facility for fretting wear testing of steam generator tubes under pressurized water up to 340 o C, is presented. The main component of the device consists in an autoclave which permits to recreate steam generator operating conditions. CAD CATIA V5R18, CAE ABAQUS and ASME Sec. VII Div. 1 (Rules for Construction of Pressure Vessels) were used along the design process. The design of the autoclave included the pressure vessel itself and the necessary flanges and nozzles. In addition, an axial dynamic sealing system was designed to allow for actuation from outside the pressure boundary. Complementary, typical tube - support contact conditions were analyzed and the principal variables affecting their mutual interaction determined. In addition, a simple device which allows performing fretting wear testing on steam generator tubes in air at room temperature was fabricated and the feasibility of a quantitative assessment of different aspects related with the fretting induced damage was explored. Characterization techniques available at Centro Atomico Bariloche, like light microscopy, scanning electron microscopy (SEM), energy dispersive analysis of X-ray (EDAX) and surface damage analysis by optic profilometry were shown to be appropriate for this aim. The designed facility will allow evaluating fretting damage of tubes - support combinations that might be used on the steam generator of the prototype reactor CAREM-25. It is also expected it could be applied to characterize fretting severity in other applications (nuclear fuel elements) (author)

  14. Broadband Light-Harvesting Molecular Triads with High FRET Efficiency Based on the Coumarin-Rhodamine-BODIPY Platform.

    Science.gov (United States)

    He, Longwei; Zhu, Sasa; Liu, Yong; Xie, Yinan; Xu, Qiuyan; Wei, Haipeng; Lin, Weiying

    2015-08-17

    Broadband capturing and FRET-based light-harvesting molecular triads, CRBs, based on the coumarin-rhodamine-BODIPY platform were rationally designed and synthesized. The absorption band of CRBs starts from blue-green to yellow-orange regions (330-610 nm), covering the strong radiation scope of sunlight. The peripheral coumarin and BODIPY chromophore energy could transfer to the central acceptor rhodamine by a one-step direct way. The energy of the coumarin moiety could also transfer to the BODIPY unit, subsequently transferring to the rhodamine core by two-step sequential ways. Both the efficiencies of the coumarin moiety and the BODIPY unit to the rhodamine core in CRBs, determined by two different ways, are very high. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Semiconductor quantum dots as Förster resonance energy transfer donors for intracellularly-based biosensors

    Science.gov (United States)

    Field, Lauren D.; Walper, Scott A.; Susumu, Kimihiro; Oh, Eunkeu; Medintz, Igor L.; Delehanty, James B.

    2017-02-01

    Förster resonance energy transfer (FRET)-based assemblies currently comprise a significant portion of intracellularly based sensors. Although extremely useful, the fluorescent protein pairs typically utilized in such sensors are still plagued by many photophysical issues including significant direct acceptor excitation, small changes in FRET efficiency, and limited photostability. Luminescent semiconductor nanocrystals or quantum dots (QDs) are characterized by many unique optical properties including size-tunable photoluminescence, broad excitation profiles coupled to narrow emission profiles, and resistance to photobleaching, which can cumulatively overcome many of the issues associated with use of fluorescent protein FRET donors. Utilizing QDs for intracellular FRET-based sensing still requires significant development in many areas including materials optimization, bioconjugation, cellular delivery and assay design and implementation. We are currently developing several QD-based FRET sensors for various intracellular applications. These include sensors targeting intracellular proteolytic activity along with those based on theranostic nanodevices for monitoring drug release. The protease sensor is based on a unique design where an intracellularly expressed fluorescent acceptor protein substrate assembles onto a QD donor following microinjection, forming an active complex that can be monitored in live cells over time. In the theranostic configuration, the QD is conjugated to a carrier protein-drug analogue complex to visualize real-time intracellular release of the drug from its carrier in response to an external stimulus. The focus of this talk will be on the design, properties, photophysical characterization and cellular application of these sensor constructs.

  16. Pairing symmetries of several iron-based superconductor families and some similarities with cuprates and heavy-fermions

    Directory of Open Access Journals (Sweden)

    Das Tanmoy

    2012-03-01

    Full Text Available We show that, by using the unit-cell transformation between 1 Fe per unit cell to 2 Fe per unit cell, one can qualitatively understand the pairing symmetry of several families of iron-based superconductors. In iron-pnictides and iron-chalcogenides, the nodeless s±-pairing and the resulting magnetic resonance mode transform nicely between the two unit cells, while retaining all physical properties unchanged. However, when the electron-pocket disappears from the Fermi surface with complete doping in KFe2As2, we find that the unit-cell invariant requirement prohibits the occurrence of s±-pairing symmetry (caused by inter-hole-pocket nesting. However, the intra-pocket nesting is compatible here, which leads to a nodal d-wave pairing. The corresponding Fermi surface topology and the pairing symmetry are similar to Ce-based heavy-fermion superconductors. Furthermore, when the Fermi surface hosts only electron-pockets in KyFe2-xSe2, the inter-electron-pocket nesting induces a nodeless and isotropic d-wave pairing. This situation is analogous to the electron-doped cuprates, where the strong antiferromagnetic order creates similar disconnected electron-pocket Fermi surface, and hence nodeless d-wave pairing appears. The unit-cell transformation in KyFe2-xSe2 exhibits that the d-wave pairing breaks the translational symmetry of the 2 Fe unit cell, and thus cannot be realized unless a vacancy ordering forms to compensate for it. These results are consistent with the coexistence picture of a competing order and nodeless d-wave superconductivity in both cuprates and KyFe1.6Se2.

  17. Fast event recorder utilizing a CCD analog shift register

    International Nuclear Information System (INIS)

    Ducar, R.J.; McIntyre, P.M.

    1978-01-01

    A system of electronics has been developed to allow the capture and recording of relatively fast, low-amplitude analog events. The heart of the system is a dual 455-cell analog shift register charge-coupled device, Fairchild CCD321ADC-3. The CCD is operated in a dual clock mode. The input is sampled at a selectable clock rate of .25-20 MHz. The stored analog data is then clocked out at a slower rate, typically about .25 MHz. The time base expansion of the analog data allows for analog-to-digital conversion and memory storage using conventional medium-speed devices. The digital data is sequentially loaded into a static RAM and may then be block transferred to a computer. The analog electronics are housed in a single-width NIM module, and the RAM memory in a single-width CAMAC module. Each pair of modules provides six parallel channels. Cost is about $200.00 per channel. Applications are described for ionization imaging (TPC, IRC) and long-drift calorimetry in liquid argon

  18. Tracking cognitive phases in analogical reasoning with event-related potentials.

    Science.gov (United States)

    Maguire, Mandy J; McClelland, M Michelle; Donovan, Colin M; Tillman, Gail D; Krawczyk, Daniel C

    2012-03-01

    Analogical reasoning consists of multiple phases. Four-term analogies (A:B::C:D) have an encoding period in which the A:B pair is evaluated prior to a mapping phase. The electrophysiological timing associated with analogical reasoning has remained unclear. We used event-related potentials to identify neural timing related to analogical reasoning relative to perceptual and semantic control conditions. Spatiotemporal principal-components analyses revealed differences primarily in left frontal electrodes during encoding and mapping phases of analogies relative to the other conditions. The timing of the activity differed depending upon the phase of the problem. During the encoding of A:B terms, analogies elicited a positive deflection compared to the control conditions between 400 and 1,200 ms, but for the mapping phase analogical processing elicited a negative deflection that occurred earlier and for a shorter time period, between 350 and 625 ms. These results provide neural and behavioral evidence that 4-term analogy problems involve a highly active evaluation phase of the A:B pair. 2012 APA, all rights reserved

  19. MnO2 nanosheet mediated "DD-A" FRET binary probes for sensitive detection of intracellular mRNA.

    Science.gov (United States)

    Ou, Min; Huang, Jin; Yang, Xiaohai; Quan, Ke; Yang, Yanjing; Xie, Nuli; Wang, Kemin

    2017-01-01

    The donor donor-acceptor (DD-A) FRET model has proven to have a higher FRET efficiency than donor-acceptor acceptor (D-AA), donor-acceptor (D-A), and donor donor-acceptor acceptor (DD-AA) FRET models. The in-tube and in-cell experiments clearly demonstrate that the "DD-A" FRET binary probes can indeed increase the FRET efficiency and provide higher imaging contrast, which is about one order of magnitude higher than the ordinary "D-A" model. Furthermore, MnO 2 nanosheets were employed to deliver these probes into living cells for intracellular TK1 mRNA detection because they can adsorb ssDNA probes, penetrate across the cell membrane and be reduced to Mn 2+ ions by intracellular GSH. The results indicated that the MnO 2 nanosheet mediated "DD-A" FRET binary probes are capable of sensitive and selective sensing gene expression and chemical-stimuli changes in gene expression levels in cancer cells. We believe that the MnO 2 nanosheet mediated "DD-A" FRET binary probes have the potential as a simple but powerful tool for basic research and clinical diagnosis.

  20. An ad-hoc fretting wear tribotester design for thin steel wires

    Directory of Open Access Journals (Sweden)

    Llavori Iñigo

    2018-01-01

    Full Text Available Steel wire ropes experience fretting wear damage when the rope runs over a sheave promoting an oscillatory motion between the wires. Consequently, wear scars appear between the contacting wires leading to an increase of the stress field and the following rupture of the wires due to fatigue. That is why the understanding and prediction of the fretting wear phenomena of thin wires is fundamental in order to improve the performance of steel wire ropes. The present research deals with the design of an ad-hoc fretting wear test machine for thin wires. The test apparatus is designed for testing thin wires with a maximum diameter of 1.0 mm, at slip amplitudes ranging from 5 to 300 μm, crossing angle between 0-90°, and contacting force ranging from 0,5 to 5 N. The working principle of displacement amplitude and contacting force as well as the crossing angle between the wires are described. Preliminary studies for understanding the fretting wear characteristics are presented, analysing 0.45 mm diameter cold-drawn eutectoid carbon steel (0.8% C wires (tensile strength higher than 3000 MPa.

  1. EXPERIMENTAL INVESTIGTION OF THE FRETTING PHENOMENON-DEPENDENCE OF NUMBERS CYCLES

    Directory of Open Access Journals (Sweden)

    Ştefan GHIMISI

    2014-12-01

    Full Text Available The present paper argues that adhesion forces and elastic deformation in the contact zone may contribute significantly to the relative displacement during fretting of metals. A simultaneously applied tangential force and normal into contact appears a adhesion force. A tangential force whose magnitude is less equal on greater than the force of limiting friction will not give rise on give rise to a sliding motion.It is determined the energy loss dissipated per fretting cycle.

  2. Parallel multispot smFRET analysis using an 8-pixel SPAD array

    Science.gov (United States)

    Ingargiola, A.; Colyer, R. A.; Kim, D.; Panzeri, F.; Lin, R.; Gulinatti, A.; Rech, I.; Ghioni, M.; Weiss, S.; Michalet, X.

    2012-02-01

    Single-molecule Förster resonance energy transfer (smFRET) is a powerful tool for extracting distance information between two fluorophores (a donor and acceptor dye) on a nanometer scale. This method is commonly used to monitor binding interactions or intra- and intermolecular conformations in biomolecules freely diffusing through a focal volume or immobilized on a surface. The diffusing geometry has the advantage to not interfere with the molecules and to give access to fast time scales. However, separating photon bursts from individual molecules requires low sample concentrations. This results in long acquisition time (several minutes to an hour) to obtain sufficient statistics. It also prevents studying dynamic phenomena happening on time scales larger than the burst duration and smaller than the acquisition time. Parallelization of acquisition overcomes this limit by increasing the acquisition rate using the same low concentrations required for individual molecule burst identification. In this work we present a new two-color smFRET approach using multispot excitation and detection. The donor excitation pattern is composed of 4 spots arranged in a linear pattern. The fluorescent emission of donor and acceptor dyes is then collected and refocused on two separate areas of a custom 8-pixel SPAD array. We report smFRET measurements performed on various DNA samples synthesized with various distances between the donor and acceptor fluorophores. We demonstrate that our approach provides identical FRET efficiency values to a conventional single-spot acquisition approach, but with a reduced acquisition time. Our work thus opens the way to high-throughput smFRET analysis on freely diffusing molecules.

  3. Spanish Velar-Insertion and Analogy: A Usage-Based Diachronic Analysis

    Science.gov (United States)

    Fondow, Steven Richard

    2010-01-01

    The theory of Analogical and Exemplar Modeling (AEM) suggests renewed discussion of the formalization of analogy and its possible incorporation in linguistic theory. AEM is a usage-based model founded upon Exemplar Modeling (Bybee 2007, Pierrehumbert 2001) that utilizes several principles of the Analogical Modeling of Language (Skousen 1992, 1995,…

  4. Fretting friction and wear characteristics of magnetorheological fluid under different magnetic field strengths

    International Nuclear Information System (INIS)

    Zhang, P.; Lee, K.H.; Lee, C.H.

    2017-01-01

    A magnetorheological fluid (MRF) performs differently under different magnetic field strength. This study examined the fretting friction and wear characteristics of MRFs under a range of magnetic field strengths and oscillation frequencies. The fretting friction and wear behaviors of MRF are investigated using a fretting friction and wear tester. The surfaces of specimen are examined by optical microscopy and 3D surface profilometer before and after the tests and wear surface profiles, the wear volume loss and wear coefficient for each magnetic field strength are evaluated. The results show that the friction and wear properties of MRF change according to the magnetic field strength and oscillation frequency. - Highlights: • Fretting friction and wear characteristics of MRF is examined. • The friction coefficients increased with increasing magnetic field strength. • The coefficient of friction decreased with increasing oscillation frequency. • Wear volume and coefficient become worse with increasing magnetic field strength.

  5. Fretting and Corrosion Damage in Taper Adapter Sleeves for Ceramic Heads: A Retrieval Study.

    Science.gov (United States)

    MacDonald, Daniel W; Chen, Antonia F; Lee, Gwo-Chin; Klein, Gregg R; Mont, Michael A; Kurtz, Steven M; Cates, Harold E; Kraay, Matthew J; Rimnac, Clare M

    2017-09-01

    During revision surgery with a well-fixed stem, a titanium sleeve can be used in conjunction with a ceramic head to achieve better stress distribution across the taper surface. In vitro testing suggests that corrosion is not a concern in sleeved ceramic heads; however, little is known about the in vivo fretting corrosion of the sleeves. The purpose of this study was to investigate fretting corrosion in sleeved ceramic heads in retrieved total hip arthroplasties. Thirty-seven sleeved ceramic heads were collected during revision. The femoral heads and sleeves were implanted 0.0-3.3 years. The implants were revised predominantly for instability, infection, and loosening. Fifty percent of the retrievals were implanted during a primary surgery. Fretting corrosion was assessed using the Goldberg-Higgs semiquantitative scoring system. Mild-to-moderate fretting corrosion scores (score = 2-3) were observed in 92% of internal tapers, 19% of external tapers, and 78% of the stems. Severe fretting corrosion was observed in 1 stem trunnion that was previously retained during revision surgery and none of the retrieved sleeves. There was no difference in corrosion damage of sleeves used in primary or revision surgery. The fretting corrosion scores in this study were predominantly mild and lower than reported fretting scores of cobalt-chrome heads in metal-on-polyethylene bearings. Although intended for use in revisions, we found that the short-term in vivo corrosion behavior of the sleeves was similar in both primary and revision surgery applications. From an in vivo corrosion perspective, sleeves are a reasonable solution for restoring the stem taper during revision surgery. Copyright © 2017. Published by Elsevier Inc.

  6. Experimental and Numerical Investigations of Fretting Fatigue Behavior for Steel Q235 Single-Lap Bolted Joints

    Directory of Open Access Journals (Sweden)

    Yazhou Xu

    2016-01-01

    Full Text Available This work aims to investigate the fretting fatigue life and failure mode of steel Q235B plates in single-lap bolted joints. Ten specimens were prepared and tested to fit the S-N curve. SEM (scanning electron microscope was then employed to observe fatigue crack surfaces and identify crack initiation, crack propagation, and transient fracture zones. Moreover, a FEM model was established to simulate the stress and displacement fields. The normal contact stress, tangential contact stress, and relative slipping displacement at the critical fretting zone were used to calculate FFD values and assess fretting fatigue crack initiation sites, which were in good agreement with SEM observations. Experimental results confirmed the fretting fatigue failure mode for these specimens. It was found that the crack initiation resulted from wear regions at the contact surfaces between plates, and fretting fatigue cracks occurred at a certain distance away from hole edges. The proposed FFD-N relationship is an alternative approach to evaluate fretting fatigue life of steel plates in bolted joints.

  7. Homo-FRET imaging as a tool to quantify protein and lipid clustering.

    Science.gov (United States)

    Bader, Arjen N; Hoetzl, Sandra; Hofman, Erik G; Voortman, Jarno; van Bergen en Henegouwen, Paul M P; van Meer, Gerrit; Gerritsen, Hans C

    2011-02-25

    Homo-FRET, Förster resonance energy transfer between identical fluorophores, can be conveniently measured by observing its effect on the fluorescence anisotropy. This review aims to summarize the possibilities of fluorescence anisotropy imaging techniques to investigate clustering of identical proteins and lipids. Homo-FRET imaging has the ability to determine distances between fluorophores. In addition it can be employed to quantify cluster sizes as well as cluster size distributions. The interpretation of homo-FRET signals is complicated by the fact that both the mutual orientations of the fluorophores and the number of fluorophores per cluster affect the fluorescence anisotropy in a similar way. The properties of the fluorescence probes are very important. Taking these properties into account is critical for the correct interpretation of homo-FRET signals in protein- and lipid-clustering studies. This is be exemplified by studies on the clustering of the lipid raft markers GPI and K-ras, as well as for EGF receptor clustering in the plasma membrane. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Establishing a cellular FRET-based fluorescence plate reader assay to monitor proNGF-induced cross-linking of sortilin and the neurotrophin receptor p75(NTR)

    DEFF Research Database (Denmark)

    Skeldal, Sune; Kjaergaard, Maj M; Alwasel, Saleh

    2015-01-01

    the vps10p domain receptor sortilin and the neurotrophin receptor p75(NTR). However, proNGF-induced receptor complex formation has been difficult to directly assess other than by western blotting. We here describe a fluorescence resonance energy transfer (FRET) based fluorescence plate reader assay...

  9. Experimental fretting-wear studies of steam generator materials

    International Nuclear Information System (INIS)

    Fisher, N.J.; Chow, A.B.; Weckwerth, M.K.

    1994-01-01

    Flow-induced vibration of steam generator tubes results in fretting-wear damage due to impacting and rubbing of the tubes against their supports. This damage can be predicted by computing tube response to flow-induced excitation forces using analytical techniques, and then relating this response to resultant wear damage using experimentally-derived wear coefficients. Fretting-wear of steam generator materials has been studied experimentally at Chalk River Laboratories for two decades. Tests are conducted in machines that simulate steam generator environmental conditions and tube-to-support dynamic interactions. Different tube and support materials, tube-to-support clearances and tube support geometries have been studied. As well, the effect of environmental conditions, such as temperature, oxygen content, pH and chemistry control additive, have been investigated. Early studies showed that damage was related to contact force as long as other parameters, such as geometry and motion were held constant. Later studies have shown that damage is related to a parameter called work-rate, which combines both contact force and sliding distance. Results of short- and long-term fretting-wear tests for CANDU steam generator materials at realistic environmental conditions are presented. These results demonstrate that work-rate is appropriate correlating parameter for impact-sliding interaction

  10. Aspects of fretting wear of sprayed cermet coatings

    International Nuclear Information System (INIS)

    Chivers, T.C.

    1985-01-01

    Two experimental fretting programmes which investigated aspects of fretting wear of sprayed cermet coatings are reviewed. These programmes were conducted in support of components used in the advanced gas-cooled reactor. It is speculated that the results from these programmes are compatible with a simple two-stage wear model. This model assumes that an initial wear process occurs which is dominated by an interlocking and removal of asperities. Such a phase will be dependent on the superficial contact areas and possibly the interfacial load, but the latter aspect is not considered. This initial wear is of very short duration and is followed by a mild, oxidative, wear mode. Coatings data are also compared with those for structural steels. In short-term low temperature tests it appears that structural steels have comparable performance with the cermet coatings but it is argued that this is an artefact of the wear process. However, at high temperatures (600 0 C) wear of stainless steel could not be determined, the specimens showing a net weight gain. It is concluded that for in-reactor fretting applications cermet coatings will have advantages over structural steels at low temperatures. Even in high temperature regions some operation at low temperatures is experienced and consequently cermet coatings may be useful here also. (orig.)

  11. Directed Evolution to Engineer Monobody for FRET Biosensor Assembly and Imaging at Live-Cell Surface.

    Science.gov (United States)

    Limsakul, Praopim; Peng, Qin; Wu, Yiqian; Allen, Molly E; Liang, Jing; Remacle, Albert G; Lopez, Tyler; Ge, Xin; Kay, Brian K; Zhao, Huimin; Strongin, Alex Y; Yang, Xiang-Lei; Lu, Shaoying; Wang, Yingxiao

    2018-04-19

    Monitoring enzymatic activities at the cell surface is challenging due to the poor efficiency of transport and membrane integration of fluorescence resonance energy transfer (FRET)-based biosensors. Therefore, we developed a hybrid biosensor with separate donor and acceptor that assemble in situ. The directed evolution and sequence-function analysis technologies were integrated to engineer a monobody variant (PEbody) that binds to R-phycoerythrin (R-PE) dye. PEbody was used for visualizing the dynamic formation/separation of intercellular junctions. We further fused PEbody with the enhanced CFP and an enzyme-specific peptide at the extracellular surface to create a hybrid FRET biosensor upon R-PE capture for monitoring membrane-type-1 matrix metalloproteinase (MT1-MMP) activities. This biosensor revealed asymmetric distribution of MT1-MMP activities, which were high and low at loose and stable cell-cell contacts, respectively. Therefore, directed evolution and rational design are promising tools to engineer molecular binders and hybrid FRET biosensors for monitoring molecular regulations at the surface of living cells. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Property-Based Monitoring of Analog and Mixed-Signal Systems

    Science.gov (United States)

    Havlicek, John; Little, Scott; Maler, Oded; Nickovic, Dejan

    In the recent past, there has been a steady growth of the market for consumer embedded devices such as cell phones, GPS and portable multimedia systems. In embedded systems, digital, analog and software components are combined on a single chip, resulting in increasingly complex designs that introduce richer functionality on smaller devices. As a consequence, the potential insertion of errors into a design becomes higher, yielding an increasing need for automated analog and mixed-signal validation tools. In the purely digital setting, formal verification based on properties expressed in industrial specification languages such as PSL and SVA is nowadays successfully integrated in the design flow. On the other hand, the validation of analog and mixed-signal systems still largely depends on simulation-based, ad-hoc methods. In this tutorial, we consider some ingredients of the standard verification methodology that can be successfully exported from digital to analog and mixed-signal setting, in particular property-based monitoring techniques. Property-based monitoring is a lighter approach to the formal verification, where the system is seen as a "black-box" that generates sets of traces, whose correctness is checked against a property, that is its high-level specification. Although incomplete, monitoring is effectively used to catch faults in systems, without guaranteeing their full correctness.

  13. Residual stress relaxation due to fretting fatigue in shot peened surfaces of Ti-6Al-4V

    International Nuclear Information System (INIS)

    Martinez, S.A.; Blodgett, M.P.; Mall, S.; Sathish, S.; Namjoshi, S.

    2003-01-01

    Fretting fatigue occurs at locations where the materials are sliding against each other under load. In order to enhance the fatigue life under fretting conditions the surface of the component is shot peened. In general, the shot peening process produces a compressive stress on the surface of the material, thereby increasing the resistance of the material to crack initiation. This paper presents the relaxation of residual stress caused during fretting fatigue. X-ray diffraction has been utilized as the method to measure residual stress in fretting fatigued samples of Ti-6Al-4V

  14. Calculated and experimental research of WWER-1000 assembly vibration and fretting damage

    International Nuclear Information System (INIS)

    Drozdov, Y.; Afanasyev, A.; Makarov, V.; Tutnov, A.; Tutnov, A.; Alekseev, E.

    2008-01-01

    The report covers the methods and results of the latest analytical and experimental studies of fretting corrosion and natural vibrations of a WWER-1000 reactor fuel assemblies (FA). The process of fretting-corrosion was investigated using a multi-specimen facility that simulated fragments of fuel rod-to-spacer grid and lower support grid mating units. A computational model was developed for vibrations in the mechanical system of a fuel rod fragment and a spacer grid fragment. A calculational and experimental modal analysis of a FA was performed. Natural frequencies, modes and decrements of FA vibrations were determined and a satisfactory coincidence of analytical and experimental results was obtained. The assessment of fretting-corrosion process dynamics was made and its dependences on operational factors were obtained. (authors)

  15. Approximate stresses in 2-D flat elastic contact fretting problems

    Science.gov (United States)

    Urban, Michael Rene

    Fatigue results from the cyclic loading of a solid body. If the body subject to fatigue is in contact with another body and relative sliding motion occurs between these two bodies, then rubbing surface damage can accelerate fatigue failure. The acceleration of fatigue failure is especially important if the relative motion between the two bodies results in surface damage without excessive surface removal via wear. The situation just described is referred to as fretting fatigue. Understanding of fretting fatigue is greatly enhanced if the stress state associated with fretting can be characterized. For Hertzian contact, this can readily be done. Unfortunately, simple stress formulae are not available for flat body contact. The primary result of the present research is the development of a new, reasonably accurate, approximate closed form expression for 2-dimensional contact stresses which has been verified using finite element modeling. This expression is also combined with fracture mechanics to provide a simple method of determining when a crack is long enough to no longer be affected by the contact stress field. Lower bounds on fatigue life can then easily be calculated using fracture mechanics. This closed form expression can also be used to calculate crack propagation within the contact stress field. The problem of determining the cycles required to generate an initial crack and what to choose as an initial crack size is unresolved as it is in non-fretting fatigue.

  16. Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.

    Science.gov (United States)

    Miyoshi, Daisuke; Nakamura, Kaori; Tateishi-Karimata, Hisae; Ohmichi, Tatsuo; Sugimoto, Naoki

    2009-03-18

    It has been revealed recently that molecular crowding, which is one of the largest differences between in vivo and in vitro conditions, is a critical factor determining the structure, stability, and function of nucleic acids. However, the effects of molecular crowding on Watson-Crick and Hoogsteen base pairs remain unclear. In order to investigate directly and quantitatively the molecular crowding effects on base pair types in nucleic acids, we designed intramolecular parallel- and antiparallel-stranded DNA duplexes consisting of Hoogsteen and Watson-Crick base pairs, respectively, as well as an intramolecular parallel-stranded triplex containing both types of base pairs. Thermodynamic analyses demonstrated that the values of free energy change at 25 degrees C for Hoogsteen base-pair formations decreased from +1.45 +/- 0.15 to +1.09 +/- 0.13 kcal mol(-1), and from -1.89 +/- 0.13 to -2.71 +/- 0.11 kcal mol(-1) in the intramolecular duplex and triplex, respectively, when the concentration of PEG 200 (polyethylene glycol with average molecular weight 200) increased from 0 to 20 wt %. However, corresponding values for Watson-Crick formation in the duplex and triplex increased from -10.2 +/- 0.2 to -8.7 +/- 0.1 kcal mol(-1), and from -10.8 +/- 0.2 to -9.2 +/- 0.2 kcal mol(-1), respectively. Furthermore, it was revealed that the opposing effects of molecular crowding on the Hoogsteen and Watson-Crick base pairs were due to different behaviors of water molecules binding to the DNA strands.

  17. In vitro simulation of fretting-corrosion in hip implant modular junctions: The influence of pH.

    Science.gov (United States)

    Royhman, Dmitry; Patel, Megha; Jacobs, Joshua J; Wimmer, Markus A; Hallab, Nadim J; Mathew, Mathew T

    2018-02-01

    The fretting-corrosion behavior of mixed metal contacts is affected by various mechanical and electrochemical parameters. Crevice conditions at the junction and patient-specific pathologies can affect the pH of the prosthetic environment. The main objective of this study is to understand the effect of pH variation at the stem/head junction of the hip implant under fretting corrosion exposure. We hypothesized that pH will have a significant influence on the fretting-corrosion behavior hip implant modular junctions. A custom-made setup was used to evaluate the fretting corrosion behavior of hip implant modular junctions. A Newborn calf serum solution (30 g/L protein content) was used to simulate the synovial fluid environment. A sinusoidal fretting motion, with a displacement amplitude of +50 µm, was applied to the Ti alloy rod. The effects of pathology driven, periprosthetic pH variation were simulated at four different pH levels (3.0, 4.5, 6.0 and 7.6). Electrochemical and mechanical properties were evaluated before, during, and after the applied fretting motion. The impedance of the system was increased in response to the fretting motion. The hysteresis tangential load/displacement behavior was not affected by pH level. The worn surfaces of CoCrMo pins exhibited the presence of tribolayer or organic deposits, in the pH 4.5 group, which may explain the lower drop in potential and mass loss observed in that group. Mechanically dominated wear mechanisms, namely, adhesive wear was shown in the pH 7.6 group, which may account for a higher potential drop and metal content loss. This study suggests that the fretting-corrosion mechanisms in hip implant are affected by the pH levels of the surrounding environment and patient-specific factors. Copyright © 2017. Published by Elsevier Ltd.

  18. Tumor specific lung cancer diagnostics with multiplexed FRET immunoassays

    Science.gov (United States)

    Geißler, D.; Hill, D.; Löhmannsröben, H.-G.; Thomas, E.; Lavigne, A.; Darbouret, B.; Bois, E.; Charbonnière, L. J.; Ziessel, R. F.; Hildebrandt, N.

    2010-02-01

    An optical multiplexed homogeneous (liquid phase) immunoassay based on FRET from a terbium complex to eight different fluorescent dyes is presented. We achieved highly sensitive parallel detection of four different lung cancer specific tumor markers (CEA, NSE, SCC and CYFRA21-1) within a single assay and show a proof-of-principle for 5- fold multiplexing. The method is well suited for fast and low-cost miniaturized point-of-care testing as well as for highthroughput screening in a broad range of in-vitro diagnostic applications.

  19. Experimental Simulation of Flow-Induced Vibration for Developing a Grid-to-Rod Fretting Model

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Youngho; Kim, Hyungkyu; Kang, Heungseok [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2013-05-15

    GTRF margin was calculated based on the fuel reliabilities program of operating power plants. But they have not accumulated sufficient experience under challenging operating conditions to be considered proven solutions. In addition, GTRF behaviors were significantly differed according to the plant types, operating condition and fuel types. So, analytical methods to resolve GTRF degradations are considered as difficult procedures for actual application. One of the most important problems is that it is difficult to evaluate the GTRF resistance of new spacer grid under operating power plant condition. Up to now, as a consequence, compliance with the fretting wear limit (typically 10% of the cladding thickness) is checked a posteriori, through post-irradiation examination. Therefore, in this study, rod simulation method for determining GTRF resistance of new spacer grid was proposed with a specially designed wear tester. This simulator enables us to examine the spacer grid shape effect under relatively short development period. In addition, for developing GTRF model, flow-induced vibration (FIV) was measured with different major variables such as GTR clearance, flow rate, etc. Fretting wear tests of nuclear fuel rods (i. e. grid-to-rod fretting) have been performed to examine the flow rate effect by using a specially designed test section with a simulated primary coolant. Based on above results, developed FIV-wear simulator could be effective to examine the spacer grid shape effect with short development period. Further study will be discussed on the GTR clearance effect with various spacer grid shapes.

  20. Characterizing the interactions between prolyl isomerase pin1 and phosphatase inhibitor-2 in living cells with FRET and FCS

    Science.gov (United States)

    Sun, Yuansheng; Wang, Lifu; Jyothikumar, Vinod; Brautigan, David L.; Periasamy, Ammasi

    2012-03-01

    Phosphatase inhibitor-2 (I2) was discovered as a regulator of protein Ser/Thr phosphatase-1 and is conserved from yeast to human. Binding between purified recombinant I2 from different species and the prolyl isomerase Pin1 has been demonstrated with pull-down assays, size exclusion chromatography and nuclear magnetic resonance spectroscopy. Despite this, questions persist as to whether these proteins associate together in living cells. In this study, we prepared fluorescent protein (FP) fusions of I2 and Pin1 and employed both Förster Resonance Energy Transfer (FRET) and Fluorescence Correlation Spectroscopy (FCS) imaging techniques to characterize their interactions in living cells. In both intensity-based and time-resolved FRET studies, we observed FRET uniformly across whole cells co-expressing I2-Cerulean and Pin1-Venus that was significantly higher than in negative controls expressing Cerulean FP (without fusing to I2) as the FRET donor and Pin1-Venus, showing a specific interaction between I2-Cerulean and Pin1-Venus in living cells. We also observed the co-diffusion of I2-Cerulean and Pin1-mCherry in Fluorescence Cross Correlation Spectroscopy (FCCS) measurements. We further showed that I2 itself as well as I2-Pin1 formed complexes in living cells (predicted from in vitro studies) via a quantitative FRET assay, and demonstrated from FCS measurements that both I2 and Pin1 (fused to Cerulean) are highly mobile in living cells.

  1. Friction and wear properties of high-velocity oxygen fuel sprayed WC-17Co coating under rotational fretting conditions

    Science.gov (United States)

    Luo, Jun; Cai, Zhenbing; Mo, Jiliang; Peng, Jinfang; Zhu, Minhao

    2016-05-01

    Rotational fretting which exist in many engineering applications has incurred enormous economic loss. Thus, accessible methods are urgently needed to alleviate or eliminate damage by rotational fretting. Surface engineering is an effective approach that is successfully adopted to enhance the ability of components to resist the fretting damage. In this paper, using a high-velocity oxygen fuel sprayed (HVOF) technique WC-17Co coating is deposited on an LZ50 steel surface to study its properties through Vickers hardness testing, scanning electric microscope (SEM), energy dispersive X-ray spectroscopy (EDX), and X-ray diffractrometry (XRD). Rotational fretting wear tests are conducted under normal load varied from 10 N to 50 N, and angular displacement amplitudes vary from 0.125° to 1°. Wear scars are examined using SEM, EDX, optical microscopy (OM), and surface topography. The experimental results reveal that the WC-17Co coating adjusted the boundary between the partial slip regime (PSR) and the slip regime (SR) to the direction of smaller amplitude displacement. As a result, the coefficients of friction are consistently lower than the substrate's coefficients of friction both in the PSR and SR. The damage to the coating in the PSR is very slight. In the SR, the coating exhibits higher debris removal efficiency and load-carrying capacity. The bulge is not found for the coating due to the coating's higher hardness to restrain plastic flow. This research could provide experimental bases for promoting industrial application of WC-17Co coating in prevention of rotational fretting wear.

  2. Theoretical study of GC+/GC base pair derivatives

    International Nuclear Information System (INIS)

    Meng Fancui; Wang Huanjie; Xu Weiren; Liu Chengbu

    2005-01-01

    The geometries of R (R=CH 3 , CH 3 O, F, NO 2 ) substituted GC base pair derivatives and their cations have been optimized at B3LYP/6-31G* level and the substituent effects on the neutral and cationic geometric structures and energies have been discussed. The inner reorganization energies of various base pair derivatives and the native GC base pair have been calculated to discuss the substituent effects on the reorganization energy. NBO (natural bond orbital) analysis has been carried out on both the neutral and the cationic systems to investigate the differences of the charge distributions and the electronic structures. The outcomes indicate that 8-CH 3 O-G:C has the greatest reorganization energy and 8-NO 2 -G:C has the least, while the other substituted base pairs have a reorganization energy close to that of G:C. The one charge is mostly localized on guanine part after ionization and as high as 0.95e. The bond distances of N1-N3'andN2-O2' in the cationic base pair derivatives shortened and that of O6-N4' elongated as compared with the corresponding bond distances of the neutral GC base pair derivatives

  3. An experimental study on the key fretting variables for flexible marine risers

    OpenAIRE

    O’Halloran, S.M.; Harte, A.M.; Shipway, P.H.; Leen, S.B.

    2018-01-01

    This paper presents an experimental investigation into the effects of contact conformity, contact pressure and displacement amplitude on the gross-slip fretting behaviour grease-lubricated cylinder-on-flat contacts in the context of flexible marine riser pressure armour wire, and compares behaviour with that observed in unlubricated conditions. Characterisation of friction and wear is critical to fretting fatigue life prediction in flexible risers since friction directly controls trailing-edg...

  4. Theoretical analysis of noncanonical base pairing interactions in ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered ..... Full optimizations of the systems were also carried out using ... of the individual bases in the base pair through the equation.

  5. Effect of mixed alloy combinations on fretting corrosion performance of spinal screw and rod implants.

    Science.gov (United States)

    Mali, Sachin A; Singh, Vaneet; Gilbert, Jeremy L

    2017-07-01

    Spinal implants are made from a variety of materials to meet the unique mechanical demands of each application. However, the medical device community has raised concern about mixing dissimilar metals in an implant because of fear of inducing corrosion. There is a lack of systematic studies on the effects of mixing metals on performance of spinal implants, especially in fretting corrosion conditions. Hence, the goal was to determine whether mixing stainless steel (SS316L), titanium alloy (Ti6Al4V) and cobalt chromium (CoCrMo) alloy components in a spinal implant leads to any increased risk of corrosion degradation. Spinal constructs consisting of single assembly screw-connector-rod components were tested using a novel short-term cyclic fretting corrosion test method. A total of 17 alloy component combinations (comprised of SS316L, Ti6Al4V-anodized and CoCrMo alloy for rod, screws and connectors) were tested under three anatomic orientations. Spinal constructs having all SS316L were most susceptible to fretting-initiated crevice corrosion attack and showed higher average fretting currents (∼25 - 30 µA), whereas constructs containing all Ti6Al4V components were less susceptible to fretting corrosion with average fretting currents in the range of 1 - 6 µA. Mixed groups showed evidence of fretting corrosion but they were not as severe as all SS316L group. SEM results showed evidence of severe corrosion attack in constructs having SS316L components. There also did not appear to be any galvanic effects of combining alloys together. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1169-1177, 2017. © 2016 Wiley Periodicals, Inc.

  6. A graphene oxide based fluorescence resonance energy transfer (FRET) biosensor for ultrasensitive detection of botulinum neurotoxin A (BoNT/A) enzymatic activity.

    Science.gov (United States)

    Shi, Jingyu; Guo, Jiubiao; Bai, Gongxun; Chan, Chunyu; Liu, Xuan; Ye, Weiwei; Hao, Jianhua; Chen, Sheng; Yang, Mo

    2015-03-15

    Botulinum neurotoxins (BoNTs) are among the most potent toxic bacterial proteins for humans, which make them potential agents for bioterrorism. Therefore, an ultrasensitive detection of BoNTs and their active states is in great need as field-deployable systems for anti-terrorism applications. We report the construction of a novel graphene oxide (GO)-peptide based fluorescence resonance energy transfer (FRET) biosensor for ultrasensitive detection of the BoNT serotype A light chain (BoNT-LcA) protease activity. A green fluorescence protein (GFP) modified SNAP-25 peptide substrate (SNAP-25-GFP) was optimally designed and synthesized with the centralized recognition/cleavage sites. This FRET platform was constructed by covalent immobilization of peptide substrate on GO with BSA passivation which have advantages of low non-specific adsorption and high stability in protein abundant solution. BoNT-LcA can specifically cleave SNAP-25-GFP substrate covalently immobilized on GO to release the fragment with GFP. Based on fluorescence signal recovery measurement, the target BoNT-LcA was detected sensitively and selectively with the linear detection range from 1fg/mL to 1pg/mL. The limit of detection (LOD) for BoNT-LcA is around 1fg/mL. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Generalized relational matching by guinea baboons (Papio papio) in two-by-two-item analogy problems.

    Science.gov (United States)

    Fagot, Joël; Thompson, Roger K R

    2011-10-01

    Analogical reasoning is considered the hallmark of human reasoning, but some studies have demonstrated that language- and symbol-trained chimpanzees can also reason analogically. Despite the potential adaptive value of this ability, evidence from other studies strongly suggests that other nonhuman primates do not have this capacity for analogical reasoning. In our three experiments, 6 of 29 baboons acquired the ability to perform a relational matching-to-sample (RMTS) task in which pairs of shapes composed relational displays. Five of these 6 monkeys then transferred this ability to RMTS tasks using novel exemplars of identity (elements in a pair are the same) and nonidentity (elements in a pair are different) relations. This transfer occurred even on trials in which the incorrect pair shared an element with the sample pair with which it was being compared. The baboons retained this ability 12 months later. The findings from our study of symbol-naive monkeys indicate that although language and symbol training facilitate conceptual thinking in nonhuman primates, such training is not a prerequisite for analogical reasoning.

  8. Combined effects of fretting and pollutant particles on the contact resistance of the electrical connectors

    Directory of Open Access Journals (Sweden)

    Zhigang Kong

    2017-06-01

    Full Text Available Usually, when electrical connectors operate in vibration environments, fretting will be produced at the contact interfaces. In addition, serious environmental pollution particles will affect contact resistance of the connectors. The fretting will worsen the reliability of connectors with the pollutant particles. The combined effects of fretting and quartz particles on the contact resistance of the gold plating connectors are studied with a fretting test system. The results show that the frequencies have obvious effect on the contact resistance. The higher the frequency, the higher the contact resistance is. The quartz particles cause serious wear of gold plating, which make the nickel and copper layer exposed quickly to increase the contact resistance. Especially in high humidity environments, water supply certain adhesion function and make quartz particles easy to insert or cover the contact surfaces, and even cause opening resistance.

  9. A FRET-based approach for quantitative evaluation of forskolin-induced pendrin trafficking at the plasma membrane in bronchial NCI H292 cells.

    Science.gov (United States)

    Tamma, Grazia; Ranieri, Marianna; Dossena, Silvia; Di Mise, Annarita; Nofziger, Charity; Svelto, Maria; Paulmichl, Markus; Valenti, Giovanna

    2013-01-01

    Human pendrin (SLC26A4, PDS) is an integral membrane protein acting as an electroneutral anion exchanger. Loss of function mutations in pendrin protein cause Pendred syndrome, a disorder characterized by sensorineural deafness and a partial iodide organification defect that may lead to thyroid goiter. Additionally, pendrin up-regulation could play a role in the pathogenesis of several diseases including bronchial asthma and chronic obstructive pulmonary disease (COPD). Therefore, monitoring the plasma membrane abundance and trafficking of pendrin in the context of a living cell is crucially important. Trafficking of pendrin to the plasma membrane was monitored by fluorescence resonance energy transfer (FRET), a physical phenomenon occurring between two fluorophores (the FRET donor and acceptor) located in close spatial proximity. Because the efficiency of the energy transfer is inversely proportional to the sixth power of the distance between donor and acceptor, FRET is extremely sensitive to small changes in distance between the donor and acceptor and is therefore a powerful tool to determine protein-protein interactions. FRET studies revealed that forskolin-induced cAMP production is associated with a significant increase of pendrin expression at plasma membrane, which is paralleled by a decrease in intracellular pH. Pendrin transposition to the membrane is accompanied with a partial depolymerization of actin cytoskeleton via Rho-GTPase inhibition. Trafficking to the plasma membrane is critical in the regulation of pendrin activity. Therefore, reliable tools for monitoring and quantifying this phenomenon are highly desirable. © 2014 S. Karger AG, Basel.

  10. The Necessity of a New Type Test Rig for the Development of an Evaluation Method in Grid Fretting Problems

    International Nuclear Information System (INIS)

    Lee, Young-Ho; Kim, Hyung-Kyu

    2007-01-01

    A grid fretting problem is recognized as one of the most important degradation mechanisms even though the examination results of fretting experiments could be applied to the development and design of spacer grid structures. This is because it is difficult to develop a fretting wear model for a grid fretting problem due to the various wear mechanisms involved according to the mechanical and environmental variables, the contact condition with a spring/dimple and the material properties. A number of spring shapes has been developed in KAERI and their performance tests such as fretting wear, flow-induced vibration (FIV) tests, etc. have been carried out from a part unit to a full assembly scale. From the unit part fretting test results, one of the noticeable results is that the contacting force (normal load) was gradually decreased with increasing number of fretting cycles due to a depth increase and this behavior was closely related to the contacting spring shape. When considering the actual contact condition between a fuel rod and a spring/dimple, if a fretting wear progresses due to a FIV under a specific normal load exerted on the fuel rod by an elastic deformation of the spring, the contacting force between the fuel rod and dimple that are located in the opposite side should be decreased. Consequently, an evaluation of developed spacer grids against fretting wear damage should be performed with the results of 1x1 cell unit experiments because a contacting force is one of the most important variables that influences a fretting wear mechanism. The discussion was focused on the development procedure of a new test rig and its performance by using a 1x1 cell unit test rig. (authors)

  11. Fretting wear damage of HexTOOL{sup TM} composite depending on the different fibre orientations

    Energy Technology Data Exchange (ETDEWEB)

    Terekhina, S; Salvia, M; Fouvry, S [Laboratoire de Tribologie et Dynamique des Systemes, UMR CNRS ECL ENISE ENSMSE 5513, Ecole Centrale de Lyon, 69134 Ecully cedex (France); Malysheva, G; Tarasova, T, E-mail: svetlana.terekhina@ec-lyon.fr, E-mail: svetlanaterekhina@yandex.ru [Bauman Moscow State Technical University, 105005 Moscow, 5, 2nd Baumanskaya str (Russian Federation)

    2009-09-15

    The composites have drawn considerable interest in the mould processes. The vibrations and fatigue stresses induced in the moulds made evident to characterize the composite HexTOOL{sup TM} under fretting conditions. Fretting is a small-amplitude oscillatory motion between contacting surfaces. The running conditions fretting maps (RCFM) of composite at ambient conditions were established. The influence of different fiber orientations of HexTOOL{sup TM} composite on the wear kinetics was shown. An energy wear approach was developed. According to results of dynamic mechanical analysis (DMA), the viscoelastic properties of composite material were obtained.

  12. An overview of the Canadian program to investigate vibration and fretting in nuclear fuel assemblies

    International Nuclear Information System (INIS)

    Oldaker, I.E.; Lane, A.D.; Forrest, C.F.

    The development of a model that would allow the fuel designer to predict the occurrence of fretting could materially reduce the amount of development testing of a new fuel design. To achieve this, we are working in several areas: to identify and measure the phenomena that excite fuel to vibrate, and to study their relation to reactor design features; to predict the vibratory response of a fuel assembly as a function of its design and environment, and; to study the relationship between vibration and fretting to determine when vibration results in fretting. (author)

  13. Protecting AREVA ATRIUM™ BWR fuel from debris fretting failure

    International Nuclear Information System (INIS)

    Cole, Steven E.; Garner, Norman L.; Lippert, Hans-Joachim; Graebert, Rüdiger; Mollard, Pierre; Hahn, Gregory C.

    2014-01-01

    Historically, debris fretting has been the leading cause of fuel rod failure in BWR fuel assemblies, costing the industry millions of dollars in lost generation and negatively impacting the working area of plant site personnel. In this paper the focus will be on recent BWR fuel product innovation designed to eliminate debris related failures. Experience feedback from more than three decades of operation history with non-line-of-sight FUELGUARD™ lower tie plate debris filters will be presented. The development and relative effectiveness of successive generations of filtration technology will be discussed. It will be shown that modern, state of the art debris filters are an effective defense against debris fretting failure. Protective measures extend beyond inlet nozzle debris filters. The comprehensive debris resistance features built into AREVA’s newest fuel design, the ATRIUM™ 11, reduce the overall risk of debris entrapment as well as providing a degree of protection from debris that may fall down on the fuel assembly from above, e.g., during refueling operations. The positive recent experience in a debris sensitive plant will be discussed showing that the combination of advanced fuel technology and a robust foreign material exclusion program at the reactor site can eliminate the debris fretting failure mechanism. (author)

  14. Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET

    Science.gov (United States)

    Hardin, John W.; Warnasooriya, Chandani; Kondo, Yasushi; Nagai, Kiyoshi; Rueda, David

    2015-01-01

    In large ribonucleoprotein machines, such as ribosomes and spliceosomes, RNA functions as an assembly scaffold as well as a critical catalytic component. Protein binding to the RNA scaffold can induce structural changes, which in turn modulate subsequent binding of other components. The spliceosomal U4/U6 di-snRNP contains extensively base paired U4 and U6 snRNAs, Snu13, Prp31, Prp3 and Prp4, seven Sm and seven LSm proteins. We have studied successive binding of all protein components to the snRNA duplex during di-snRNP assembly by electrophoretic mobility shift assay and accompanying conformational changes in the U4/U6 RNA 3-way junction by single-molecule FRET. Stems I and II of the duplex were found to co-axially stack in free RNA and function as a rigid scaffold during the entire assembly, but the U4 snRNA 5′ stem-loop adopts alternative orientations each stabilized by Prp31 and Prp3/4 binding accounting for altered Prp3/4 binding affinities in presence of Prp31. PMID:26503251

  15. The spatiotemporal pattern of Src activation at lipid rafts revealed by diffusion-corrected FRET imaging.

    Directory of Open Access Journals (Sweden)

    Shaoying Lu

    2008-07-01

    Full Text Available Genetically encoded biosensors based on fluorescence resonance energy transfer (FRET have been widely applied to visualize the molecular activity in live cells with high spatiotemporal resolution. However, the rapid diffusion of biosensor proteins hinders a precise reconstruction of the actual molecular activation map. Based on fluorescence recovery after photobleaching (FRAP experiments, we have developed a finite element (FE method to analyze, simulate, and subtract the diffusion effect of mobile biosensors. This method has been applied to analyze the mobility of Src FRET biosensors engineered to reside at different subcompartments in live cells. The results indicate that the Src biosensor located in the cytoplasm moves 4-8 folds faster (0.93+/-0.06 microm(2/sec than those anchored on different compartments in plasma membrane (at lipid raft: 0.11+/-0.01 microm(2/sec and outside: 0.18+/-0.02 microm(2/sec. The mobility of biosensor at lipid rafts is slower than that outside of lipid rafts and is dominated by two-dimensional diffusion. When this diffusion effect was subtracted from the FRET ratio images, high Src activity at lipid rafts was observed at clustered regions proximal to the cell periphery, which remained relatively stationary upon epidermal growth factor (EGF stimulation. This result suggests that EGF induced a Src activation at lipid rafts with well-coordinated spatiotemporal patterns. Our FE-based method also provides an integrated platform of image analysis for studying molecular mobility and reconstructing the spatiotemporal activation maps of signaling molecules in live cells.

  16. Fluorescence resonance energy transfer (FRET) in chemistry and ...

    Indian Academy of Sciences (India)

    Förster distance dependence of the FRET rate. SANGEETA SAINI,1 HARJINDER SINGH2 and BIMAN BAGCHI1,*. 1Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012. 2Permanent address: Department of ...

  17. Rapid genotyping using pyrene-perylene locked nucleic acid complexes

    DEFF Research Database (Denmark)

    Kumar, Santhosh T.; Myznikova, Anna; Samokhina, Evgeniya

    2013-01-01

    We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene-perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific...... geometry of the pyrene fluorophore attached to the 2'-amino group of 2'-amino-LNA in position 4 allows for the first time to efficiently utilize dipole-dipole orientation parameter for sensing of single-nucleotide polymorphisms (SNPs) in nucleic acid targets by FRET. Using novel probes, SNP detection......-perylene FRET pairs, e.g., in imaging and clinical diagnostics....

  18. Ratiometric FRET-based detection of DNA and micro-RNA on the surface using TIRF detection

    International Nuclear Information System (INIS)

    Matveeva, Evgenia G.; Gryczynski, Zygmunt; Stewart, Donald R.; Gryczynski, Ignacy

    2010-01-01

    A new FRET-based method for the ratiometric detection of DNA oligomers on a surface using TIRF detection mode is reported. The dual-labeled system consisting of two hybridized oligomers, Cy3oligoY:Cy5oligoX was immobilized on the surface, and the total internal reflection fluorescence (TIRF) was used to detect emission signals from the surface. Two signals, green and red, which originated from the green donor Cy3 and the red acceptor Cy5, have been simultaneously detected. When the target single-stranded complimentary oligomer was present in the solution, this oligomer replaced the Cy3oligoY in the donor:acceptor complex on the surface and the ratio of red-to-green signal was dramatically changed. This detection scheme is generally applicable to the detection of DNA or RNA on a surface.

  19. A combined experimental and finite element approach to analyse the fretting mechanism of the head-stem taper junction in total hip replacement.

    Science.gov (United States)

    Bitter, Thom; Khan, Imran; Marriott, Tim; Lovelady, Elaine; Verdonschot, Nico; Janssen, Dennis

    2017-09-01

    Fretting corrosion at the taper interface of modular hip implants has been implicated as a possible cause of implant failure. This study was set up to gain more insight in the taper mechanics that lead to fretting corrosion. The objectives of this study therefore were (1) to select experimental loading conditions to reproduce clinically relevant fretting corrosion features observed in retrieved components, (2) to develop a finite element model consistent with the fretting experiments and (3) to apply more complicated loading conditions of activities of daily living to the finite element model to study the taper mechanics. The experiments showed similar wear patterns on the taper surface as observed in retrievals. The finite element wear score based on Archard's law did not correlate well with the amount of material loss measured in the experiments. However, similar patterns were observed between the simulated micromotions and the experimental wear measurements. Although the finite element model could not be validated, the loading conditions based on activities of daily living demonstrate the importance of assembly load on the wear potential. These findings suggest that finite element models that do not incorporate geometry updates to account for wear loss may not be appropriate to predict wear volumes of taper connections.

  20. A combined wear-fatigue design methodology for fretting in the pressure armour layer of flexible marine risers

    OpenAIRE

    O'Halloran, S.M.; Shipway, P.H.; Connaire, A.D.; Leen, Sean B.; Harte, A.M.

    2017-01-01

    This paper presents a combined experimental and computational methodology for fretting wear-fatigue prediction of pressure armour wire in flexible marine risers. Fretting wear, friction and fatigue parameters of pressure armour material have been characterised experimentally. A combined fretting wear-fatigue finite element model has been developed using an adaptive meshing technique and the effect of bending-induced tangential slip has been characterised. It has been shown that a surface dama...

  1. Fretting-corrosion behavior in hip implant modular junctions: The influence of friction energy and pH variation.

    Science.gov (United States)

    Royhman, Dmitry; Patel, Megha; Runa, Maria J; Wimmer, Markus A; Jacobs, Joshua J; Hallab, Nadim J; Mathew, Mathew T

    2016-09-01

    Recently, there has been increasing concern in the orthopedic community over the use of hip implant modular devices due to an increasing number of reports of early failure, failure that has been attributed to fretting-corrosion at modular interfaces. Much is still unknown about the electrochemical and mechanical degradation mechanisms associated with the use of such devices. Accordingly, the purpose of our study was to develop a methodology for testing the fretting-corrosion behavior of modular junctions. A fretting-corrosion apparatus was used to simulate the fretting-corrosion conditions of a CoCrMo hip implant head on a Ti6Al4V hip implant stem. The device features two perpendicularly-loaded CoCrMo pins that articulated against a Ti6Al4V rod. A sinusoidal fretting motion was applied to the rod at various displacement amplitudes (25, 50, 100, 150 and 200μm) at a constant load of 200N. Bovine calf serum at two different pH levels (3.0 and 7.6) was used to simulate the fluid environment around the joint. Experiments were conducted in two modes of electrochemical control - free-potential and potentiostatic. Electrochemical impedance spectroscopy tests were done before and after the fretting motion to assess changes in corrosion kinetics. In free potential mode, differences were seen in change in potential as a function of displacement amplitude. In general, VDrop (the drop in potential at the onset of fretting), VFretting, (the average potential during fretting), ΔVFretting (the change in potential from the onset of fretting to its termination) and VRecovery (the change in potential from the termination of fretting until stabilization) appeared linear at both pH levels, but showed drastic deviation from linearity at 100μm displacement amplitude. Subsequent EDS analysis revealed a large number of Ti deposits on the CoCrMo pin surfaces. Potentiostatic tests at both pH levels generally showed increasing current with increasing displacement amplitude. Electrochemical

  2. On the geometry of the fuel rod supports concerning a fretting wear failure

    International Nuclear Information System (INIS)

    Kim, Hyung-Kyu; Lee, Young-Ho; Lee, Kang-Hee

    2008-01-01

    Geometrical conditions of spacer grid springs and dimples of a light water reactor fuel assembly are studied in this paper concerning a fuel rod's fretting wear failure. In this framework, the springs/dimples are categorized from the aspects of their orientation with respect to the fuel axis and the contact types. Possible motions on the contacts between the springs/dimples and fuel rods are estimated by conducting a flow-induced vibration test. Features of the wear scar and depth are investigated by independent fretting wear tests carried out with spring and dimple specimens of typical contact geometries. It is also attempted here to apply the contact mechanics theory to a fuel fretting wear analysis such as the prediction of a wear depth profile and its rate, which is influenced by the contact shape of the springs/dimples. It is shown that the theory can be applied to a dimensional control of a coining for the springs/dimples, which is usually carried out in a thin plate fabrication. From the results, the necessary conditions for a spring/dimple geometry for restraining a fretting wear failure are discussed

  3. Analog Circuit Design Optimization Based on Evolutionary Algorithms

    Directory of Open Access Journals (Sweden)

    Mansour Barari

    2014-01-01

    Full Text Available This paper investigates an evolutionary-based designing system for automated sizing of analog integrated circuits (ICs. Two evolutionary algorithms, genetic algorithm and PSO (Parswal particle swarm optimization algorithm, are proposed to design analog ICs with practical user-defined specifications. On the basis of the combination of HSPICE and MATLAB, the system links circuit performances, evaluated through specific electrical simulation, to the optimization system in the MATLAB environment, for the selected topology. The system has been tested by typical and hard-to-design cases, such as complex analog blocks with stringent design requirements. The results show that the design specifications are closely met. Comparisons with available methods like genetic algorithms show that the proposed algorithm offers important advantages in terms of optimization quality and robustness. Moreover, the algorithm is shown to be efficient.

  4. Theoretical-experimental analysis of the fretting/impact wear in fuel rods

    International Nuclear Information System (INIS)

    Pecos, Luis F.

    2001-01-01

    Nuclear power plant fuel elements are subjected to flow induced vibrations. A consequence of these vibrations is impact/fretting wear in fuel rods or sliding shoes. Because of the difficulties to assert the mechanism of impact/fretting wear phenomenon it is necessary to use semiempirical formulations in order to predict the wear rate of the components. The results of a series of experiments with Zr-4 specimens are presented in this work. A parameter called 'work-rate' was used to normalize the wear rates and interpret the results in terms of wear coefficient. (author) [es

  5. Application of Influence Function Method to the Fretting Wear Problems

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Choon Yeol; Tian, Li Si; Bae, Joon Woo; Chai, Young Suck [Yeungnam University, Gyongsan (Korea, Republic of)

    2006-07-01

    Numerical analysis by influence function method (IFM) is demonstrated in this study in order to investigate the fretting wear problems on the secondary side of the steam generator, caused by flow induced vibration. Two-dimensional numerical contact model in terms of Cauchy integral equation is developed. The distributions of normal pressures, shear stresses and displacement fields are derived between two contact bodies which have similar elastic properties. The work rate model is adopted to find the wear amounts between two materials. The results are compared with the solutions by finite element analyses, which show the utilization of the present method to the fretting wear problems.

  6. Application of Influence Function Method to the Fretting Wear Problems

    International Nuclear Information System (INIS)

    Lee, Choon Yeol; Tian, Li Si; Bae, Joon Woo; Chai, Young Suck

    2006-01-01

    Numerical analysis by influence function method (IFM) is demonstrated in this study in order to investigate the fretting wear problems on the secondary side of the steam generator, caused by flow induced vibration. Two-dimensional numerical contact model in terms of Cauchy integral equation is developed. The distributions of normal pressures, shear stresses and displacement fields are derived between two contact bodies which have similar elastic properties. The work rate model is adopted to find the wear amounts between two materials. The results are compared with the solutions by finite element analyses, which show the utilization of the present method to the fretting wear problems

  7. In Situ Probing Intracellular Drug Release from Redox-Responsive Micelles by United FRET and AIE.

    Science.gov (United States)

    Wang, Xuelin; Li, Juanjuan; Yan, Qi; Chen, Yanrui; Fan, Aiping; Wang, Zheng; Zhao, Yanjun

    2018-03-01

    Redox-responsive micelles are versatile nanoplatforms for on-demand drug delivery, but the in situ evaluation of drug release is challenging. Fluorescence resonance energy transfer (FRET) technique shows potential for addressing this, while the aggregation-caused quenching effect limits the assay sensitivity. The aim of the current work is to combine aggregation-induced emission (AIE) probe with FRET to realize drug release assessment from micelles. Tetraphenylethene (TPE) is selected as AIE dye and curcumin (Cur) is chosen as the model drug as well as FRET receptor. The drug is covalently linked to a block copolymer via the disulfide bond linker and TPE is also chemically linked to the polymer via an amide bond; the obtained amphiphilic polymer conjugate self-assembles into micelles with a hydrodynamic size of ≈125 nm. Upon the supplement of glutathione or tris(2-carboxyethyl)phosphine) trigger (10 × 10 -3 m), the drug release induces the fluorescence increase of both TPE and Cur. Accompanied with the FRET decay, absorption enhancement and particle size increase are observed. The same phenomenon is observed in MCF-7 cells. The FRET-AIE approach can be a useful addition to the spectrum of available methods for monitoring drug release from stimuli-responsive nanomedicine. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Bayesian analogy with relational transformations.

    Science.gov (United States)

    Lu, Hongjing; Chen, Dawn; Holyoak, Keith J

    2012-07-01

    How can humans acquire relational representations that enable analogical inference and other forms of high-level reasoning? Using comparative relations as a model domain, we explore the possibility that bottom-up learning mechanisms applied to objects coded as feature vectors can yield representations of relations sufficient to solve analogy problems. We introduce Bayesian analogy with relational transformations (BART) and apply the model to the task of learning first-order comparative relations (e.g., larger, smaller, fiercer, meeker) from a set of animal pairs. Inputs are coded by vectors of continuous-valued features, based either on human magnitude ratings, normed feature ratings (De Deyne et al., 2008), or outputs of the topics model (Griffiths, Steyvers, & Tenenbaum, 2007). Bootstrapping from empirical priors, the model is able to induce first-order relations represented as probabilistic weight distributions, even when given positive examples only. These learned representations allow classification of novel instantiations of the relations and yield a symbolic distance effect of the sort obtained with both humans and other primates. BART then transforms its learned weight distributions by importance-guided mapping, thereby placing distinct dimensions into correspondence. These transformed representations allow BART to reliably solve 4-term analogies (e.g., larger:smaller::fiercer:meeker), a type of reasoning that is arguably specific to humans. Our results provide a proof-of-concept that structured analogies can be solved with representations induced from unstructured feature vectors by mechanisms that operate in a largely bottom-up fashion. We discuss potential implications for algorithmic and neural models of relational thinking, as well as for the evolution of abstract thought. Copyright 2012 APA, all rights reserved.

  9. A FRET-Based Approach for Quantitative Evaluation of Forskolin-Induced Pendrin Trafficking at the Plasma Membrane in Bronchial NCI H292 Cells

    Directory of Open Access Journals (Sweden)

    Grazia Tamma

    2013-12-01

    Full Text Available Background: Human pendrin (SLC26A4, PDS is an integral membrane protein acting as an electroneutral anion exchanger. Loss of function mutations in pendrin protein cause Pendred syndrome, a disorder characterized by sensorineural deafness and a partial iodide organification defect that may lead to thyroid goiter. Additionally, pendrin up-regulation could play a role in the pathogenesis of several diseases including bronchial asthma and chronic obstructive pulmonary disease (COPD. Therefore, monitoring the plasma membrane abundance and trafficking of pendrin in the context of a living cell is crucially important. Methods: Trafficking of pendrin to the plasma membrane was monitored by fluorescence resonance energy transfer (FRET, a physical phenomenon occurring between two fluorophores (the FRET donor and acceptor located in close spatial proximity. Because the efficiency of the energy transfer is inversely proportional to the sixth power of the distance between donor and acceptor, FRET is extremely sensitive to small changes in distance between the donor and acceptor and is therefore a powerful tool to determine protein-protein interactions. Results: FRET studies revealed that forskolin-induced cAMP production is associated with a significant increase of pendrin expression at plasma membrane, which is paralleled by a decrease in intracellular pH. Pendrin transposition to the membrane is accompanied with a partial depolymerization of actin cytoskeleton via Rho-GTPase inhibition. Conclusion: Trafficking to the plasma membrane is critical in the regulation of pendrin activity. Therefore, reliable tools for monitoring and quantifying this phenomenon are highly desirable.

  10. Advanced KSNP fuel, plus7 : grid-to-rod fretting wear resistance of the plus7 spacer grids

    International Nuclear Information System (INIS)

    Kim, Kyu Tae; Kim, Yong Hwan; Jang, Young Ki; Choi, Joon Hyung

    2003-01-01

    Vibration-induced grid-to-rod fretting wear initiates at a certain critical gap correlated with a critical work rate. A critical gap between grid and rod forms due to in-reactor performance of fuel, thermal relaxation of grid spring and irradiation growth of grid strap, etc. A critical work rate may be generated by three vibration mechanisms proposed in this paper. Three vibration mechanisms have been derived with various fretting wear experience in commercial reactors as well as various out-of-pile hydraulic test results. The first active vibration mechanism is high turbulence-induced excessive fuel rod vibration with the combination of excessive grid-to-rod gap. The second active vibration mechanism is self-excited fuel assembly vibration in a low frequency range caused by hydraulically unbalanced mixing vanes of the spacer grid assembly. The third active vibration mechanism is self-excited spacer grid strap vibration in quite a high frequency range caused by some spacer grid designs. In this study, each vibration mechanism on the grid-to-rod fretting wear damage is discussed. On the other hand, the effects of various grid designs on the fretting wear damage in the commercial reactors are predicted using the long-term fretting wear test results. It is found that the larger grid-to-rod initial contact area generates the less fretting wear damage. Consequently the conformal spring of PLUS7 is superior to typical convex shaped spring with regard to fretting wear resistance since the former generates relatively larger contact area than the latter

  11. FRET analysis of CP12 structural interplay by GAPDH and PRK.

    Science.gov (United States)

    Moparthi, Satish Babu; Thieulin-Pardo, Gabriel; de Torres, Juan; Ghenuche, Petru; Gontero, Brigitte; Wenger, Jérôme

    2015-03-13

    CP12 is an intrinsically disordered protein playing a key role in the regulation of the Benson-Calvin cycle. Due to the high intrinsic flexibility of CP12, it is essential to consider its structural modulation induced upon binding to the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) enzymes. Here, we report for the first time detailed structural modulation about the wild-type CP12 and its site-specific N-terminal and C-terminal disulfide bridge mutants upon interaction with GAPDH and PRK by Förster resonance energy transfer (FRET). Our results indicate an increase in CP12 compactness when the complex is formed with GAPDH or PRK. In addition, the distributions in FRET histograms show the elasticity and conformational flexibility of CP12 in all supra molecular complexes. Contrarily to previous beliefs, our FRET results importantly reveal that both N-terminal and C-terminal site-specific CP12 mutants are able to form the monomeric (GAPDH-CP12-PRK) complex. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Spectroscopic and theoretical investigation of conformational changes of proteins by synthesized pyrimidine derivative and its sensitivity towards FRET application

    Science.gov (United States)

    Ghosh, Swadesh; Singharoy, Dipti; Bhattacharya, Subhash Chandra

    2018-04-01

    Interest in synthesizing and characterizing (IR, NMR and HRMS spectroscopic methods) a pyrimidine based Schiff-base ligand, 2-(2-(Anthracen-9-ylmethylene) hydrazinyl)-4,6-dimethyl pyrimidine (ANHP) has been developed for its application to ascertain the conformational change of protein and sensitivity towards fluorescence resonance energy transfer (FRET) process. Location of ANHP in bovine serum albumin (BSA) and human serum albumin (HSA) proteins environment has been determined using different spectroscopic techniques. Weakly fluorescent ANHP have shown greater protein induced fluorescence enhancement (PIFE) in case of HSA than BSA, though in both cases energy transfer efficiency are almost same but difference in binding constant values encourages us to find the location of ANHP within the complex protein environment. From the FRET parameter and α-helicity change, it has been found that ANHP bound with Trp-214 of HSA and surface Trp-134 of BSA. Conformational changes of proteins have been observed more for HSA than BSA in presence of ANHP, which has confirmed the location of ANHP in both the protein environments. Coupled with experimental studies, molecular docking analysis has also been done to explain the locations and distance dependent FRET process of ANHP in both proteins.

  13. A New Generation of FRET Sensors for Robust Measurement of Gαi1, Gαi2 and Gαi3 Activation Kinetics in Single Cells.

    Directory of Open Access Journals (Sweden)

    Jakobus van Unen

    Full Text Available G-protein coupled receptors (GPCRs can activate a heterotrimeric G-protein complex with subsecond kinetics. Genetically encoded biosensors based on Förster resonance energy transfer (FRET are ideally suited for the study of such fast signaling events in single living cells. Here we report on the construction and characterization of three FRET biosensors for the measurement of Gαi1, Gαi2 and Gαi3 activation. To enable quantitative long-term imaging of FRET biosensors with high dynamic range, fluorescent proteins with enhanced photophysical properties are required. Therefore, we use the currently brightest and most photostable CFP variant, mTurquoise2, as donor fused to Gαi subunit, and cp173Venus fused to the Gγ2 subunit as acceptor. The Gαi FRET biosensors constructs are expressed together with Gβ1 from a single plasmid, providing preferred relative expression levels with reduced variation in mammalian cells. The Gαi FRET sensors showed a robust response to activation of endogenous or over-expressed alpha-2A-adrenergic receptors, which was inhibited by pertussis toxin. Moreover, we observed activation of the Gαi FRET sensor in single cells upon stimulation of several GPCRs, including the LPA2, M3 and BK2 receptor. Furthermore, we show that the sensors are well suited to extract kinetic parameters from fast measurements in the millisecond time range. This new generation of FRET biosensors for Gαi1, Gαi2 and Gαi3 activation will be valuable for live-cell measurements that probe Gαi activation.

  14. Silver(I)-Mediated Base Pairs in DNA Sequences Containing 7-Deazaguanine/Cytosine: towards DNA with Entirely Metallated Watson-Crick Base Pairs.

    Science.gov (United States)

    Méndez-Arriaga, José M; Maldonado, Carmen R; Dobado, José A; Galindo, Miguel A

    2018-03-26

    DNA sequences comprising noncanonical 7-deazaguanine ( 7C G) and canonical cytosine (C) are capable of forming Watson-Crick base pairs via hydrogen bonds as well as silver(I)-mediated base pairs by coordination to central silver(I) ions. Duplexes I and II containing 7C G and C have been synthesized and characterized. The incorporation of silver(I) ions into these duplexes has been studied by means of temperature-dependent UV spectroscopy, circular dichroism, and DFT calculations. The results suggest the formation of DNA molecules comprising contiguous metallated 7C G-Ag I -C Watson-Crick base pairs that preserve the original B-type conformation. Furthermore, additional studies performed on duplex III indicated that, in the presence of Ag I ions, 7C G-C and 7C A-T Watson-Crick base pairs ( 7C A, 7-deazadenine; T, thymine) can be converted to metallated 7C G-Ag I -C and 7C A-Ag I -T base pairs inside the same DNA molecule whilst maintaining its initial double helix conformation. These findings are very important for the development of customized silver-DNA nanostructures based on a Watson-Crick complementarity pattern. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions.

    Science.gov (United States)

    Götz, Markus; Wortmann, Philipp; Schmid, Sonja; Hugel, Thorsten

    2018-01-30

    Single-molecule Förster resonance energy transfer (smFRET) has become a widely used biophysical technique to study the dynamics of biomolecules. For many molecular machines in a cell proteins have to act together with interaction partners in a functional cycle to fulfill their task. The extension of two-color to multi-color smFRET makes it possible to simultaneously probe more than one interaction or conformational change. This not only adds a new dimension to smFRET experiments but it also offers the unique possibility to directly study the sequence of events and to detect correlated interactions when using an immobilized sample and a total internal reflection fluorescence microscope (TIRFM). Therefore, multi-color smFRET is a versatile tool for studying biomolecular complexes in a quantitative manner and in a previously unachievable detail. Here, we demonstrate how to overcome the special challenges of multi-color smFRET experiments on proteins. We present detailed protocols for obtaining the data and for extracting kinetic information. This includes trace selection criteria, state separation, and the recovery of state trajectories from the noisy data using a 3D ensemble Hidden Markov Model (HMM). Compared to other methods, the kinetic information is not recovered from dwell time histograms but directly from the HMM. The maximum likelihood framework allows us to critically evaluate the kinetic model and to provide meaningful uncertainties for the rates. By applying our method to the heat shock protein 90 (Hsp90), we are able to disentangle the nucleotide binding and the global conformational changes of the protein. This allows us to directly observe the cooperativity between the two nucleotide binding pockets of the Hsp90 dimer.

  16. Burst pressure and leak rate from fretted SG tubes

    International Nuclear Information System (INIS)

    Hwang, Seong Sik; Jung, Man Kyo; Kim, Hong Pyo; Kim, Joung Soo

    2005-01-01

    Steam generator(SG) tubes of a pressurized water reactor(PWR) have suffered from various types of corrosion, such as pitting, wastage and stress corrosion cracking (SCC) on both the primary and secondary side. Recently, fretting/wear degradation at the tube support region has been reported in some Korean nuclear power plants. In order to prevent the primary coolant from leaking to the secondary side, the tubes are repaired by a sleeving or plugging. It is important to establish the repair criteria to assure a reactor integrity and yet maintain the plugging ratio within the limits needed for an efficient operation. The objective of the burst test is to obtain a relationship between the burst/leak rate and the shape of the fretted flaws machined with an electro discharge machining (EDM)

  17. A high-throughput fluorescence resonance energy transfer (FRET)-based endothelial cell apoptosis assay and its application for screening vascular disrupting agents

    International Nuclear Information System (INIS)

    Zhu, Xiaoming; Fu, Afu; Luo, Kathy Qian

    2012-01-01

    Highlights: ► An endothelial cell apoptosis assay using FRET-based biosensor was developed. ► The fluorescence of the cells changed from green to blue during apoptosis. ► This method was developed into a high-throughput assay in 96-well plates. ► This assay was applied to screen vascular disrupting agents. -- Abstract: In this study, we developed a high-throughput endothelial cell apoptosis assay using a fluorescence resonance energy transfer (FRET)-based biosensor. After exposure to apoptotic inducer UV-irradiation or anticancer drugs such as paclitaxel, the fluorescence of the cells changed from green to blue. We developed this method into a high-throughput assay in 96-well plates by measuring the emission ratio of yellow fluorescent protein (YFP) to cyan fluorescent protein (CFP) to monitor the activation of a key protease, caspase-3, during apoptosis. The Z′ factor for this assay was above 0.5 which indicates that this assay is suitable for a high-throughput analysis. Finally, we applied this functional high-throughput assay for screening vascular disrupting agents (VDA) which could induce endothelial cell apoptosis from our in-house compounds library and dioscin was identified as a hit. As this assay allows real time and sensitive detection of cell apoptosis, it will be a useful tool for monitoring endothelial cell apoptosis in living cell situation and for identifying new VDA candidates via a high-throughput screening.

  18. Four-gate transistor analog multiplier circuit

    Science.gov (United States)

    Mojarradi, Mohammad M. (Inventor); Blalock, Benjamin (Inventor); Cristoloveanu, Sorin (Inventor); Chen, Suheng (Inventor); Akarvardar, Kerem (Inventor)

    2011-01-01

    A differential output analog multiplier circuit utilizing four G.sup.4-FETs, each source connected to a current source. The four G.sup.4-FETs may be grouped into two pairs of two G.sup.4-FETs each, where one pair has its drains connected to a load, and the other par has its drains connected to another load. The differential output voltage is taken at the two loads. In one embodiment, for each G.sup.4-FET, the first and second junction gates are each connected together, where a first input voltage is applied to the front gates of each pair, and a second input voltage is applied to the first junction gates of each pair. Other embodiments are described and claimed.

  19. The paired-domination and the upper paired-domination numbers of graphs

    Directory of Open Access Journals (Sweden)

    Włodzimierz Ulatowski

    2015-01-01

    Full Text Available In this paper we continue the study of paired-domination in graphs. A paired-dominating set, abbreviated PDS, of a graph \\(G\\ with no isolated vertex is a dominating set of vertices whose induced subgraph has a perfect matching. The paired-domination number of \\(G\\, denoted by \\(\\gamma_{p}(G\\, is the minimum cardinality of a PDS of \\(G\\. The upper paired-domination number of \\(G\\, denoted by \\(\\Gamma_{p}(G\\, is the maximum cardinality of a minimal PDS of \\(G\\. Let \\(G\\ be a connected graph of order \\(n\\geq 3\\. Haynes and Slater in [Paired-domination in graphs, Networks 32 (1998, 199-206], showed that \\(\\gamma_{p}(G\\leq n-1\\ and they determine the extremal graphs \\(G\\ achieving this bound. In this paper we obtain analogous results for \\(\\Gamma_{p}(G\\. Dorbec, Henning and McCoy in [Upper total domination versus upper paired-domination, Questiones Mathematicae 30 (2007, 1-12] determine \\(\\Gamma_{p}(P_n\\, instead in this paper we determine \\(\\Gamma_{p}(C_n\\. Moreover, we describe some families of graphs \\(G\\ for which the equality \\(\\gamma_{p}(G=\\Gamma_{p}(G\\ holds.

  20. Effects of Plasma ZrN Metallurgy and Shot Peening Duplex Treatment on Fretting Wear and Fretting Fatigue Behavior of Ti6Al4V Alloy.

    Science.gov (United States)

    Tang, Jingang; Liu, Daoxin; Zhang, Xiaohua; Du, Dongxing; Yu, Shouming

    2016-03-23

    A metallurgical zirconium nitride (ZrN) layer was fabricated using glow metallurgy using nitriding with zirconiuming prior treatment of the Ti6Al4V alloy. The microstructure, composition and microhardness of the corresponding layer were studied. The influence of this treatment on fretting wear (FW) and fretting fatigue (FF) behavior of the Ti6Al4V alloy was studied. The composite layer consisted of an 8-μm-thick ZrN compound layer and a 50-μm-thick nitrogen-rich Zr-Ti solid solution layer. The surface microhardness of the composite layer is 1775 HK 0.1 . A gradient in cross-sectional microhardness distribution exists in the layer. The plasma ZrN metallurgical layer improves the FW resistance of the Ti6Al4V alloy, but reduces the base FF resistance. This occurs because the improvement in surface hardness results in lowering of the toughness and increasing in the notch sensitivity. Compared with shot peening treatment, plasma ZrN metallurgy and shot peening composite treatment improves the FW resistance and enhances the FF resistance of the Ti6Al4V alloy. This is attributed to the introduction of a compressive stress field. The combination of toughness, strength, FW resistance and fatigue resistance enhance the FF resistance for titanium alloy.

  1. Fis protein induced λF-DNA bending observed by single-pair fluorescence resonance energy transfer

    Science.gov (United States)

    Chi-Cheng, Fu; Wunshain, Fann; Yuan Hanna, S.

    2006-03-01

    Fis, a site-specific DNA binding protein, regulates many biological processes including recombination, transcription, and replication in E.coli. Fis induced DNA bending plays an important role in regulating these functions and bending angle range from ˜50 to 95 dependent on the DNA sequence. For instance, the average bending angle of λF-DNA (26 bp, 8.8nm long, contained λF binding site on the center) measured by gel mobility shift assays was ˜ 94 . But the traditional method cannot provide information about the dynamics and the angle distribution. In this study, λF-DNA was labeled with donor (Alexa Fluor 546) and acceptor (Alexa Fluor 647) dyes on its two 5' ends and the donor-acceptor distances were measured using single-pair fluorescence resonance energy transfer (sp-FRET) with and without the present of Fis protein. Combing with structure information of Fis-DNA complex, the sp-FRET results are used to estimate the protein induced DNA bending angle distribution and dynamics.

  2. Simulation of vibration modes of the fuel rod damaged due to the grid-to-rod fretting wear

    International Nuclear Information System (INIS)

    Kim, Kyu Tae; Kim, Kyeong Koo; Jang, Young Ki; Lee, Kyou Seok

    1997-01-01

    The flow-induced fuel fretting wear observed in some PWRs mainly proceeds in the grid-to-rod contact positions. The grid-to-rod fretting wear in the PWR fuel assembly depends on grid-to-rod gap size, its axial profile and flow-induced vibration. This paper describes the GRIDFORCE program which generates the axially dependent grid-to-rod gap size as a function of burnup. The axially dependent grid-to-rod gap profiles are employed to predict the fuel rod vibration mode shapes by the ANSYS code. With the help of the Paidousis empirical formula, this paper also calculates the fuel rod vibration amplitudes under various supporting conditions, which indicates that the increase of the number of unsupported mid-grids will increase the fuel rod vibration amplitude. On the other hand, the comparison of the predicted vibration mode shapes and the observed mid-grid fretting wear pattern indicates that the 1st and 6th vibration mode shapes under the supporting inactive condition at the mid-grids can simulate the observed mid-grid fretting wear profile. This paper also proposes design guidelines against the grid-to-rod fretting wear. (author). 3 refs., 8 figs

  3. Learning preferences from paired opposite-based semantics

    DEFF Research Database (Denmark)

    Franco de los Ríos, Camilo; Rodríguez, J. Tinguaro; Montero, Javier

    2017-01-01

    Preference semantics examine the meaning of the preference predicate, according to the way that alternatives can be understood and organized for decision making purposes. Through opposite-based semantics, preference structures can be characterized by their paired decomposition of preference...... on the character of opposition, the compound meaning of preference emerges from the fuzzy reinforcement of paired opposite concepts, searching for significant evidence for affirming dominance among the decision objects. Here we propose a general model for the paired decomposition of preference, examining its...

  4. Fretting Corrosion Behavior of Experimental Ti-20Cr Compared to Titanium.

    Science.gov (United States)

    Sawada, Tomofumi; Schille, Christine; Almadani, Atif; Geis-Gerstorfer, Jürgen

    2017-02-17

    Experimental cast titanium alloys containing 20 mass% chromium (Ti-20Cr) show preferable mechanical properties and a good corrosion resistance. This study evaluated the fretting corrosion behavior of Ti-20Cr. Ti-20Cr ( n = 4) and commercially pure titanium (CP-Ti, n = 6) disk specimens were used. The fretting corrosion test was performed by electrochemical corrosion at 0.3 V in 0.9% saline solution and mechanical damage using 10 scratching cycles with three different scratching speeds (10-40 mm/s) at 10 N. After testing, the activation peak, repassivation time and surface morphology of each specimen were analyzed. The differences between the results were tested by parametric tests (α = 0.05). The average activation peaks were significantly higher in CP-Ti than in Ti-20Cr ( p Ti. Slight differences in the repassivation time were observed between the materials at every scratching speed; faster scratching speeds showed shorter repassivation times in both materials ( p Ti showed severe damage and significantly higher wear depth than Ti-20Cr ( p < 0.05). In conclusion, adding chromium to titanium reduced surface damage and improved the fretting corrosion resistance.

  5. Widespread Transient Hoogsteen Base-Pairs in Canonical Duplex DNA with Variable Energetics

    Science.gov (United States)

    Alvey, Heidi S.; Gottardo, Federico L.; Nikolova, Evgenia N.; Al-Hashimi, Hashim M.

    2015-01-01

    Hoogsteen base-pairing involves a 180 degree rotation of the purine base relative to Watson-Crick base-pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction, and replication. Here, using Nuclear Magnetic Resonance R1ρ relaxation dispersion, we show that transient Hoogsteen base-pairs occur across more diverse sequence and positional contexts than previously anticipated. We observe sequence-specific variations in Hoogsteen base-pair energetic stabilities that are comparable to variations in Watson-Crick base-pair stability, with Hoogsteen base-pairs being more abundant for energetically less favorable Watson-Crick base-pairs. Our results suggest that the variations in Hoogsteen stabilities and rates of formation are dominated by variations in Watson-Crick base pair stability, suggesting a late transition state for the Watson-Crick to Hoogsteen conformational switch. The occurrence of sequence and position-dependent Hoogsteen base-pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions. PMID:25185517

  6. Determination of a Wear Initiation Cycle by using a Contact Resistance Measurement in Nuclear Fuel Fretting

    International Nuclear Information System (INIS)

    Lee, Young Ho; Kim, Hyung Kyu

    2008-01-01

    In nuclear fuel fretting, the improving of the contact condition with a modified spring shape is a useful method for increasing the wear resistance of the nuclear fuel rod. This is because the fretting wear resistance between the fuel rod and grid spring is mainly affected by the grid spring shape rather than the environment, the contact modes, etc. In addition, the wear resistance is affected by the wear debris behavior between contact surfaces. So, it is expected that the wear initiation of each spring shape should be determined in order to evaluate a wear resistance. However, it is almost impossible to measure the wear behavior in contact surfaces on a real time basis because the contact surfaces are always hidden. Besides, the results of the worn surface observation after the fretting wear tests are restricted to archive the information on the wear debris behavior and the formation mechanism of the wear scar. In order to evaluate the wear behavior during the fretting wear tests, it is proposed that the contact resistance measurement is a useful method for examining the wear initiation cycle and modes. Generally, fretting wear damages are rapidly progressed by a localized plastic deformation between the contact surfaces, crack initiation and fracture of the deformed surface with a strain hardening difference between a surface and a subsurface and finally a detachment of wear debris. After this, wear debris is easily oxidized by frictional heat, test environment, etc. At this time, a small amount of electric current applied between the contact surfaces will be influenced by the wear debris, which could be an obstacle to an electric current flow. So, it is possible to archive the information on the wear behavior by measuring the contact resistance. In order to determine the wear initiation cycle during the fretting wear tests, in this study, fretting wear tests have been performed by applying a constant electric current in room temperature air

  7. Fretting wear damage of steam generator tubes and its prediction modeling

    International Nuclear Information System (INIS)

    Che Honglong; Lei Mingkai

    2013-01-01

    The steam generator is the key equipment used for the energy transition in nuclear power plant. Since the high-temperature and high-pressure fluid flows with high speed, the steam generator tubes will be excited and vibrate, leading to the tremendous fretting wear problem on the tubes, sometimes even leading to tube cracking. This paper introduces typical fretting wear cases, the result of corresponding simulation wear experiment and damage mechanism which combining mechanical wear and erosion-corrosion. Work rate model could give a reasonable life prediction about the steam generator tube, and this predictive model has been used in nuclear power plant safety assessment. (authors)

  8. Terbium to Quantum Dot FRET Bioconjugates for Clinical Diagnostics: Influence of Human Plasma on Optical and Assembly Properties

    Directory of Open Access Journals (Sweden)

    Niko Hildebrandt

    2011-10-01

    Full Text Available Förster resonance energy transfer (FRET from luminescent terbium complexes (LTC as donors to semiconductor quantum dots (QDs as acceptors allows extraordinary large FRET efficiencies due to the long Förster distances afforded. Moreover, time-gated detection permits an efficient suppression of autofluorescent background leading to sub-picomolar detection limits even within multiplexed detection formats. These characteristics make FRET-systems with LTC and QDs excellent candidates for clinical diagnostics. So far, such proofs of principle for highly sensitive multiplexed biosensing have only been performed under optimized buffer conditions and interactions between real-life clinical media such as human serum or plasma and LTC-QD-FRET-systems have not yet been taken into account. Here we present an extensive spectroscopic analysis of absorption, excitation and emission spectra along with the luminescence decay times of both the single components as well as the assembled FRET-systems in TRIS-buffer, TRIS-buffer with 2% bovine serum albumin, and fresh human plasma. Moreover, we evaluated homogeneous LTC-QD FRET assays in QD conjugates assembled with either the well-known, specific biotin-streptavidin biological interaction or, alternatively, the metal-affinity coordination of histidine to zinc. In the case of conjugates assembled with biotin-streptavidin no significant interference with the optical and binding properties occurs whereas the histidine-zinc system appears to be affected by human plasma.

  9. A virus-MIPs fluorescent sensor based on FRET for highly sensitive detection of JEV.

    Science.gov (United States)

    Liang, Caishuang; Wang, Huan; He, Kui; Chen, Chunyan; Chen, Xiaoming; Gong, Hang; Cai, Changqun

    2016-11-01

    Major stumbling blocks in the recognition and detection of virus are the unstable biological recognition element or the complex detection means. Here a fluorescent sensor based on virus-molecular imprinted polymers (virus-MIPs) was designed for specific recognition and highly sensitive detection of Japanese encephalitis virus (JEV). The virus-MIPs were anchored on the surface of silica microspheres modified by fluorescent dye, pyrene-1-carboxaldehyde (PC). The fluorescence intensity of PC can be enhanced by the principle of fluorescence resonance energy transfer (FRET), where virus acted as energy donor and PC acted as energy acceptor. The enhanced fluorescence intensity was proportional to the concentration of virus in the range of 24-960pM, with a limit of detection (LOD, 3σ) of 9.6pM, and the relative standard deviation was 1.99%. In additional, the specificity study confirmed the resultant MIPs has high-selectivity for JEV. This sensor would become a new key for the detection of virus because of its high sensitive, simple operation, high stability and low cost. Copyright © 2016. Published by Elsevier B.V.

  10. Electrochemical deposition of magnesium from analogous ionic liquid based on dimethylformamide

    International Nuclear Information System (INIS)

    Wang, Huaiyou; Jia, Yongzhong; Wang, Xiaohua; Yao, Ying; Yue, Duyuan; Jing, Yan

    2013-01-01

    In this paper, a homogeneous, colorless analogous ionic liquid containing dimethylformamide (DMF) and magnesium chloride hexahydrate is synthesized. The conductivity of analogous ionic liquid is measured as a function of temperature and composition. Irreversible electrochemical behavior was generally observed by cyclic voltammetry (CV) in the analogous ionic liquid based electrolytes containing simple Mg salt. CV also shows that the reducing reaction of Mg 2+ is a diffusion control process. Electrochemical impedance spectroscopy (EIS) of analogous ionic liquid was measured at 20 °C, 40 °C and 60 °C. Electrodeposition of magnesium metal from analogous ionic liquid has been studied. The Mg deposits are also systematically characterized by the techniques of powder X-ray diffraction (XRD), scanning electron microscope (SEM) and energy dispersive spectroscopy (EDS). Results showed that magnesium was found in the deposited film

  11. Analog Group Delay Equalizers Design Based on Evolutionary Algorithm

    Directory of Open Access Journals (Sweden)

    M. Laipert

    2006-04-01

    Full Text Available This paper deals with a design method of the analog all-pass filter designated for equalization of the group delay frequency response of the analog filter. This method is based on usage of evolutionary algorithm, the Differential Evolution algorithm in particular. We are able to design such equalizers to be obtained equal-ripple group delay frequency response in the pass-band of the low-pass filter. The procedure works automatically without an input estimation. The method is presented on solving practical examples.

  12. A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET).

    Science.gov (United States)

    Lerner, Eitan; Ploetz, Evelyn; Hohlbein, Johannes; Cordes, Thorben; Weiss, Shimon

    2016-07-07

    Single-molecule, protein-induced fluorescence enhancement (PIFE) serves as a molecular ruler at molecular distances inaccessible to other spectroscopic rulers such as Förster-type resonance energy transfer (FRET) or photoinduced electron transfer. In order to provide two simultaneous measurements of two distances on different molecular length scales for the analysis of macromolecular complexes, we and others recently combined measurements of PIFE and FRET (PIFE-FRET) on the single molecule level. PIFE relies on steric hindrance of the fluorophore Cy3, which is covalently attached to a biomolecule of interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate. In this work, we provide a theoretical framework that accounts for relevant photophysical and kinetic parameters of PIFE-FRET, show how this framework allows the extraction of the fold-decrease in isomerization mobility from experimental data, and show how these results provide information on changes in the accessible volume of Cy3. The utility of this model is then demonstrated for experimental results on PIFE-FRET measurement of different protein-DNA interactions. The proposed model and extracted parameters could serve as a benchmark to allow quantitative comparison of PIFE effects in different biological systems.

  13. A novel pseudo-complementary PNA G-C base pair

    DEFF Research Database (Denmark)

    Olsen, Anne G.; Dahl, Otto; Petersen, Asger Bjørn

    2011-01-01

    Pseudo-complementary oligonucleotide analogues and mimics provide novel opportunities for targeting duplex structures in RNA and DNA. Previously, a pseudo-complementary A-T base pair has been introduced. Towards sequence unrestricted targeting, a pseudo-complementary G-C base pair consisting...

  14. Feedback-mediated cancer therapy: a FRET-based nanoreporter approach

    Science.gov (United States)

    Sarkar, Suproteem K.; Khater, Yashika; Kulkarni, Ashish; Sengupta, Shiladitya

    2014-08-01

    A theranostic nanoparticle system was developed by integrating a chemotherapeutic agent with an "activatable" fluorescent tracer. The system signals tumor death by monitoring the activity of caspase-3, a product of apoptosis, and can therefore screen the treatment sensitivity of a particular tumor. The polymer nanoparticles (Poly [isobutylene-alt-maleic anhydride]) were formed through reprecipitation and contained paclitaxel, a chemotherapy drug, and fluorescein isothiocyanate, a fluorescent dye. The dye's fluorescence was quenched through Förster resonance energy transfer (FRET) by a quencher that was connected to the dye by a peptide chain. With sizes ranging from 200-250 nm, the nanoparticles were stable for two weeks. The nanoparticles were tested in vitro with responsive Lewis Lung Carcinoma (LLC) cells and taxane-resistant cells. Upon cell death by paclitaxel exposure, caspase-3 cleaved the peptide chain connecting the dye and the quencher, causing the system to fluoresce. When LLC cells were treated with the system, the nanoreporters fluoresced, but when resistant cells were tested, and when the drug was removed from the system, the nanoreporters did not fluoresce. Since the system screens if a drug can successfully kill a particular tumor, it offers a novel and promising approach to personalized medicine.

  15. Nanoswitches based on DNA base pairs: why adenine-thymine is less suitable than guanine-cytosine

    NARCIS (Netherlands)

    Fonseca Guerra, C.; van der Wijst, T.; Bickelhaupt, F.M.

    2006-01-01

    Substituted Watson-Crick guanine-cytosine (GC) base pairs were recently shown to yield robust three-state nanoswitches. Here, we address the question: Can such supramolecular switches also be based on Watson-Crick adenine-thymine (AT) base pairs? We have theoretically analyzed AT pairs in which

  16. Envisaging quantum transport phenomenon in a muddled base pair of DNA

    Science.gov (United States)

    Vohra, Rajan; Sawhney, Ravinder Singh

    2018-05-01

    The effect of muddled base pair on electron transfer through a deoxyribonucleic acid (DNA) molecule connected to the gold electrodes has been elucidated using tight binding model. The effect of hydrogen and nitrogen bonds on the resistance of the base pair has been minutely observed. Using the semiempirical extended Huckel approach within NEGF regime, we have determined the current and conductance vs. bias voltage for disordered base pairs of DNA made of thymine (T) and adenine (A). The asymmetrical behaviour amid five times depreciation in the current characteristics has been observed for deviated Au-AT base pair-Au devices. An interesting revelation is that the conductance of the intrinsic AT base pair configuration attains dramatically high values with the symmetrical zig-zag pattern of current, which clearly indicates the transformation of the bond length within the strands of base pair when compared with other samples. A thorough investigation of the transmission coefficients T( E) and HOMO-LUMO gap reveals the misalignment of the strands in base pairs of DNA. The observed results present an insight to extend this work to build biosensing devices to predict the abnormality with the DNA.

  17. Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.

    Science.gov (United States)

    Szulik, Marta W; Pallan, Pradeep S; Nocek, Boguslaw; Voehler, Markus; Banerjee, Surajit; Brooks, Sonja; Joachimiak, Andrzej; Egli, Martin; Eichman, Brandt F; Stone, Michael P

    2015-02-10

    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'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) 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 A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 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 C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); 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 N(4) 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.

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

    Science.gov (United States)

    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

  19. Structured Analog CMOS Design

    CERN Document Server

    Stefanovic, Danica

    2008-01-01

    Structured Analog CMOS Design describes a structured analog design approach that makes it possible to simplify complex analog design problems and develop a design strategy that can be used for the design of large number of analog cells. It intentionally avoids treating the analog design as a mathematical problem, developing a design procedure based on the understanding of device physics and approximations that give insight into parameter interdependences. The proposed transistor-level design procedure is based on the EKV modeling approach and relies on the device inversion level as a fundament

  20. Analog synthetic biology.

    Science.gov (United States)

    Sarpeshkar, R

    2014-03-28

    We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog-digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA-protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations.

  1. Two-dimensional Forster resonance energy transfer (2-D FRET) and the membrane raft hypothesis

    OpenAIRE

    Acasandrei, Maria; Dale, Robert; VAN DE VEN, Martin; AMELOOT, Marcel

    2006-01-01

    A model for analyzing Forster resonance energy transfer (FRET) data in relation to the cell plasma membrane raft hypothesis is developed to take into account: (a) the distribution of FRET donors and acceptors at the surface of probing antibody fragments specific for a putative raft component; (b) partitioning of the raft component between raft and non-raft areas of the membrane; and (c) the dependence of the raft partition on the expression level of the considered component. Analysis of relev...

  2. Classic maximum entropy recovery of the average joint distribution of apparent FRET efficiency and fluorescence photons for single-molecule burst measurements.

    Science.gov (United States)

    DeVore, Matthew S; Gull, Stephen F; Johnson, Carey K

    2012-04-05

    We describe a method for analysis of single-molecule Förster resonance energy transfer (FRET) burst measurements using classic maximum entropy. Classic maximum entropy determines the Bayesian inference for the joint probability describing the total fluorescence photons and the apparent FRET efficiency. The method was tested with simulated data and then with DNA labeled with fluorescent dyes. The most probable joint distribution can be marginalized to obtain both the overall distribution of fluorescence photons and the apparent FRET efficiency distribution. This method proves to be ideal for determining the distance distribution of FRET-labeled biomolecules, and it successfully predicts the shape of the recovered distributions.

  3. Effect of different atmospheres on the electrical contact performance of electronic components under fretting wear

    Science.gov (United States)

    Liu, Xin-Long; Cai, Zhen-Bing; Cui, Ye; Liu, Shan-Bang; Xu, Xiao-Jun; Zhu, Min-Hao

    2018-04-01

    The effects of oxide etch on the surface morphology of metals for industrial application is a common cause of electrical contacts failure, and it has becomes a more severe problem with the miniaturization of modern electronic devices. This study investigated the effects of electrical contact resistance on the contactor under three different atmospheres (oxygen, air, and nitrogen) based on 99.9% copper/pogo pins contacts through fretting experiments. The results showed the minimum and stable electrical contact resistance value when shrouded in the nitrogen environment and with high friction coefficient. The rich oxygen environment promotes the formation of cuprous oxide, thereby the electrical contact resistance increases. Scanning electron microscope microscopy and electron probe microanalysis were used to analyze the morphology and distribution of elements of the wear area, respectively. The surface product between contacts was investigated by x-ray photoelectron spectroscopy analysis to explain the different electrical contact properties of the three tested samples during fretting.

  4. Analogy between gambling and measurement-based work extraction

    Science.gov (United States)

    Vinkler, Dror A.; Permuter, Haim H.; Merhav, Neri

    2016-04-01

    In information theory, one area of interest is gambling, where mutual information characterizes the maximal gain in wealth growth rate due to knowledge of side information; the betting strategy that achieves this maximum is named the Kelly strategy. In the field of physics, it was recently shown that mutual information can characterize the maximal amount of work that can be extracted from a single heat bath using measurement-based control protocols, i.e. using ‘information engines’. However, to the best of our knowledge, no relation between gambling and information engines has been presented before. In this paper, we briefly review the two concepts and then demonstrate an analogy between gambling, where bits are converted into wealth, and information engines, where bits representing measurements are converted into energy. From this analogy follows an extension of gambling to the continuous-valued case, which is shown to be useful for investments in currency exchange rates or in the stock market using options. Moreover, the analogy enables us to use well-known methods and results from one field to solve problems in the other. We present three such cases: maximum work extraction when the probability distributions governing the system and measurements are unknown, work extraction when some energy is lost in each cycle, e.g. due to friction, and an analysis of systems with memory. In all three cases, the analogy enables us to use known results in order to obtain new ones.

  5. A method to quantify FRET stoichiometry with phasor plot analysis and acceptor lifetime ingrowth.

    Science.gov (United States)

    Chen, WeiYue; Avezov, Edward; Schlachter, Simon C; Gielen, Fabrice; Laine, Romain F; Harding, Heather P; Hollfelder, Florian; Ron, David; Kaminski, Clemens F

    2015-03-10

    FRET is widely used for the study of protein-protein interactions in biological samples. However, it is difficult to quantify both the FRET efficiency (E) and the affinity (Kd) of the molecular interaction from intermolecular FRET signals in samples of unknown stoichiometry. Here, we present a method for the simultaneous quantification of the complete set of interaction parameters, including fractions of bound donors and acceptors, local protein concentrations, and dissociation constants, in each image pixel. The method makes use of fluorescence lifetime information from both donor and acceptor molecules and takes advantage of the linear properties of the phasor plot approach. We demonstrate the capability of our method in vitro in a microfluidic device and also in cells, via the determination of the binding affinity between tagged versions of glutathione and glutathione S-transferase, and via the determination of competitor concentration. The potential of the method is explored with simulations. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET.

    Science.gov (United States)

    Khadria, Ambalika S; Senes, Alessandro

    2015-07-01

    Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations. © 2015 Wiley Periodicals, Inc.

  7. 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.

    Science.gov (United States)

    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. Copyright © 2012 Elsevier

  8. Bosonic analog of the Klein paradox

    International Nuclear Information System (INIS)

    Wagner, R. E.; Ware, M. R.; Su, Q.; Grobe, R.

    2010-01-01

    The standard Klein paradox describes how an incoming electron scatters off a supercritical electrostatic barrier that is so strong that it can generate electron-positron pairs. This fermionic system has been widely discussed in textbooks to illustrate some of the discrepancies between quantum mechanical and quantum field theoretical descriptions for the pair creation process. We compare the fermionic dynamics with that of the corresponding bosonic system. We point out that the direct counterpart of the Pauli exclusion principle (the central mechanism to resolve the fermionic Klein paradox) is stimulated emission, which leads to the resolution of the analogous bosonic paradox.

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

    Science.gov (United States)

    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.

  10. Experimental evaluation of the fretting fatigue behavior of high-strength steel monostrands

    DEFF Research Database (Denmark)

    Winkler, Jan; Fischer, Gregor; Georgakis, Christos T.

    2013-01-01

    In this paper, the fretting fatigue behavior of pretensioned high-strength steel monostrands is investigated. A method based on the digital image correlation (DIC) technique was used to quantify the relative movement between individual wires along the length of the monostrand. The experimental data....... Moreover, the paper provides relevant information about the monostrand bending stiffness and the extent of relative displacement between core and outer wires of the monostrand undergoing flexural deformations. The results presented herein are of special interest for the fatigue analysis of modern stay...

  11. Dual Mechanism of an Intramolecular Charge Transfer (ICT)-FRET-Based Fluorescent Probe for the Selective Detection of Hydrogen Peroxide.

    Science.gov (United States)

    Liang, Xiao; Xu, Xiaoyi; Qiao, Dan; Yin, Zheng; Shang, Luqing

    2017-12-14

    A dual-mechanism intramolecular charge transfer (ICT)-FRET fluorescent probe for the selective detection of H 2 O 2 in living cells has been designed and synthesized. This probe used a coumarin-naphthalimide hybrid as the FRET platform and a boronate moiety as the recognition group. Upon the addition of H 2 O 2 , the probe exhibited a redshifted (73 nm) fluorescence emission, and the ratio of fluorescence intensities at λ=558 and 485 nm (F 558 /F 485 ) shifted notably (up to 100-fold). Moreover, there was a good linearity (R 2 =0.9911) between the ratio and concentration of H 2 O 2 in the range of 0 to 60 μm, with a limit of detection of 0.28 μm (signal to noise ratio (S/N)=3). This probe could also detect enzymatically generated H 2 O 2 . Importantly, it could be used to visualize endogenous H 2 O 2 produced by stimulation from epidermal growth factor. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Les vicissitudes du fret ferroviaire

    OpenAIRE

    DABLANC, L

    2010-01-01

    Dans beaucoup de pays européens, et plus encore en Amérique du Nord et en Asie, le transport de marchandises par le train a augmenté depuis dix ans. Cette activité réduit la part des marchandises acheminées par la route et contribue ainsi au développement durable : un camion émet 8 à 30 fois plus de dioxyde de carbone que le train, pour une distance et une quantité transportée équivalentes. Pourtant, la France a raté ce renouveau. Filiale du groupe public SNCF, la Société Fret SNCF, qui assur...

  13. Hoogsteen base pairs proximal and distal to echinomycin binding sites on DNA

    International Nuclear Information System (INIS)

    Mendel, D.; Dervan, P.B.

    1987-01-01

    Forms of the DNA double helix containing non-Watson-Crick base-pairing have been discovered recently based on x-ray diffraction analysis of quionoxaline antibiotic-oligonucleotide complexes. In an effort to find evidence for Hoogsteen base-pairing at quinoxaline-binding sites in solution, chemical footprinting (differential cleavage reactivity) of echinomycin bound to DNA restriction fragments was examined. The authors report that purines (A>G) in the first and/or fourth base-pair positions of occupied echinomycin-binding sites are hyperreactive to diethyl pyrocarbonate. The correspondence of the solid-state data and the sites of diethyl pyrocarbonate hyperreactivity suggests that diethyl pyrocarbonate may be a sensitive reagent for the detection of Hoogsteen base-pairing in solution. Moreover, a 12-base-pair segment of alternating A-T DNA, which is 6 base pairs away from the nearest strong echinomycin-binding site, is also hyperreactive to diethyl pyrocarbonate in the presence of echinomycin. This hyperreactive segment may be an altered form of right-handed DNA that is entirely Hoogsteen base-paired

  14. From Dark to Light to Fluorescence Resonance Energy Transfer (FRET): Polarity-Sensitive Aggregation-Induced Emission (AIE)-Active Tetraphenylethene-Fused BODIPY Dyes with a Very Large Pseudo-Stokes Shift.

    Science.gov (United States)

    Şen, Esra; Meral, Kadem; Atılgan, Serdar

    2016-01-11

    The work presented herein is devoted to the fabrication of large Stokes shift dyes in both organic and aqueous media by combining dark resonance energy transfer (DRET) and fluorescence resonance energy transfer (FRET) in one donor-acceptor system. In this respect, a series of donor-acceptor architectures of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) dyes substituted by one, two, or three tetraphenylethene (TPE) luminogens were designed and synthesised. The photophysical properties of these three chromophore systems were studied to provide insight into the nature of donor-acceptor interactions in both THF and aqueous media. Because the generation of emissive TPE donor(s) is strongly polarity dependent, due to its aggregation-induced emission (AIE) feature, one might expect the formation of appreciable fluorescence emission intensity with a very large pseudo-Stokes shift in aqueous media when considering FRET process. Interestingly, similar results were also recorded in THF for the chromophore systems, although the TPE fragment(s) of the dyes are non-emissive. The explanation for this photophysical behaviour lies in the DRET. This is the first report on combining two energy-transfer processes, namely, FRET and DRET, in one polarity-sensitive donor-acceptor pair system. The accuracy of the dark-emissive donor property of the TPE luminogen is also presented for the first time as a new feature for AIE phenomena. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Bandwidth tunable microwave photonic filter based on digital and analog modulation

    Science.gov (United States)

    Zhang, Qi; Zhang, Jie; Li, Qiang; Wang, Yubing; Sun, Xian; Dong, Wei; Zhang, Xindong

    2018-05-01

    A bandwidth tunable microwave photonic filter based on digital and analog modulation is proposed and experimentally demonstrated. The digital modulation is used to broaden the effective gain spectrum and the analog modulation is to get optical lines. By changing the symbol rate of data pattern, the bandwidth is tunable from 50 MHz to 700 MHz. The interval of optical lines is set according to the bandwidth of gain spectrum which is related to the symbol rate. Several times of bandwidth increase are achieved compared to a single analog modulation and the selectivity of the response is increased by 3.7 dB compared to a single digital modulation.

  16. A Series of Fluorescent and Colorimetric Chemodosimeters for Selective Recognition of Cyanide Based on the FRET Mechanism.

    Science.gov (United States)

    Hua, Ying-Xi; Shao, Yongliang; Wang, Ya-Wen; Peng, Yu

    2017-06-16

    A series of fluorescence "turn-on" probes (PY, AN, NA, B1, and B2) have been developed and successfully applied to detect cyanide anions based on the Michael addition reaction and FRET mechanism. These probes demonstrated good selectivity, high sensitivity, and very fast recognition for CN - . In particular, the fluorescence response of probe NA finished within 3 s. Low limits of detection (down to 63 nM) are also obtained in these probes with remarkable fluorescence enhancement factors. In addition, fluorescence colors of these probes turned to blue, yellow, or orange upon sensing CN - . In UV-vis mode, all of them showed ratiometric response for CN - . 1 H NMR titration experiments and TDDFT calculations were taken to verify the mechanism of the specific reaction and fluorescence properties of the corresponding compounds. Moreover, silica gel plates with these probes were also fabricated and utilized to detect cyanide.

  17. The impact of semantic distance and induced stress on analogical reasoning: a neurocomputational account.

    Science.gov (United States)

    Vendetti, Michael; Knowlton, Barbara J; Holyoak, Keith J

    2012-12-01

    In a study of reasoning with four-term verbal analogy problems, we explored the relationship between the effects of an acute, mild stressor and the complexity of the reasoning process. Participants judged whether analogy problems in the form A:B :: C:D were valid or invalid, on the basis of whether the relation in the A:B term matched that in the C:D term. Half of the problems contained a C:D pair semantically near the A:B pair (e.g., NOSE:SCENT :: TONGUE:TASTE), and the other half contained ones semantically far from A:B (e.g., NOSE:SCENT :: ANTENNA:SIGNAL). After an initial block without stress, participants were randomly assigned to count backward by 13 s from 1,000 while being told to go faster, or to count forward by 1 s from 0. The stress-induced participants reported a significant increase in state anxiety as compared to controls immediately after the mental arithmetic task. Stressed participants performed less accurately (as measured by d') on both near and far analogy problems, mainly due to an increase in false alarms. We were able to model the influence of semantic distance using the "learning and inference with schemas and analogies" (LISA) model. Our findings indicated that even mild increases in stress impair analogical reasoning. However, the decrement does not seem to directly involve the integration of relations, but rather is due to a shift in decision strategy: Under stress, people show an increased tendency to endorse analogies as valid when the terms in the individual pairs are semantically related to each other, even if the overall analogical relationship is not valid.

  18. FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein

    NARCIS (Netherlands)

    Nazarov, P.V.; Koehorst, R.B.M.; Vos, W.L.; Apanasovich, V.V.; Hemminga, M.A.

    2007-01-01

    A formalism for membrane protein structure determination was developed. This method is based on steady-state FRET data and information about the position of the fluorescence maxima on site-directed fluorescent labeled proteins in combination with global data analysis utilizing simulation-based

  19. Fretting corrosion tests on orthopedic plates and screws made of ASTM F138 stainless steel

    OpenAIRE

    Santos,Claudio Teodoro dos; Barbosa,Cássio; Monteiro,Maurício de Jesus; Abud,Ibrahim de Cerqueira; Caminha,Ieda Maria Vieira; Roesler,Carlos Rodrigo de Mello

    2015-01-01

    Introduction Although there has been significant progress in the design of implants for osteosynthesis, the occurrence of failures in these medical devices are still frequent. These implants are prone to suffer from fretting corrosion due to micromotion that takes place between the screw heads and plate holes. Consequently, fretting corrosion has been the subject of research in order to understand its influence on the structural integrity of osteosynthesis implants. The aim of this paper is t...

  20. Development of CINPA1 analogs as novel and potent inverse agonists of constitutive androstane receptor.

    Science.gov (United States)

    Lin, Wenwei; Yang, Lei; Chai, Sergio C; Lu, Yan; Chen, Taosheng

    2016-01-27

    Constitutive androstane receptor (CAR, NR1I3) and pregnane X receptor (PXR, NR1I2) are master regulators of endobiotic and xenobiotic metabolism and disposition. Because CAR is constitutively active in certain cellular contexts, inhibiting CAR might reduce drug-induced hepatotoxicity and resensitize drug-resistant cancer cells to chemotherapeutic drugs. We recently reported a novel CAR inhibitor/inverse agonist CINPA1 (11). Here, we have obtained or designed 54 analogs of CINPA1 and used a time-resolved fluorescence resonance energy transfer (TR-FRET) assay to evaluate their CAR inhibition potency. Many of the 54 analogs showed CAR inverse agonistic activities higher than those of CINPA1, which has an IC50 value of 687 nM. Among them, 72 has an IC50 value of 11.7 nM, which is about 59-fold more potent than CINPA1 and over 10-fold more potent than clotrimazole (an IC50 value of 126.9 nM), the most potent CAR inverse agonist in a biochemical assay previously reported by others. Docking studies provide a molecular explanation of the structure-activity relationship (SAR) observed experimentally. To our knowledge, this effort is the first chemistry endeavor in designing and identifying potent CAR inverse agonists based on a novel chemical scaffold, leading to 72 as the most potent CAR inverse agonist so far. The 54 chemicals presented are novel and unique tools for characterizing CAR's function, and the SAR information gained from these 54 analogs could guide future efforts to develop improved CAR inverse agonists. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  1. Fretting Wear Behaviors of Aluminum Cable Steel Reinforced (ACSR Conductors in High-Voltage Transmission Line

    Directory of Open Access Journals (Sweden)

    Xingchi Ma

    2017-09-01

    Full Text Available This work reports the fretting wear behavior of aluminum cable steel reinforced (ACSR conductors for use in high-voltage transmission line. Fretting wear tests of Al wires were conducted on a servo-controlled fatigue testing machine with self-made assistant apparatus, and their fretting process characteristics, friction force, wear damage, and wear surface morphology were detailed analyzed. The results show that the running regime of Al wires changes from a gross slip regime to a mixed regime more quickly as increasing contact load. With increasing amplitudes, gross slip regimes are more dominant under contact loads of lower than 30 N. The maximum friction force is relatively smaller in the NaCl solution than in a dry friction environment. The primary wear mechanisms in dry friction environments are abrasive wear and adhesive wear whereas abrasive wear and fatigue damage are dominant in NaCl solution.

  2. Plant a tree in cyberspace: metaphor and analogy as design elements in Web-based learning environments.

    Science.gov (United States)

    Wolfe, C R

    2001-02-01

    Analogy and metaphor are figurative forms of communication that help people integrate new information with prior knowledge to facilitate comprehension and appropriate inferences. The novelty and versatility of the Web place cognitive burdens on learners that can be overcome through the use of analogies and metaphors. This paper explores three uses of figurative communication as design elements in Web-based learning environments, and provides empirical illustrations of each. First, extended analogies can be used as the basis of cover stories that create an analogy between the learner's position and a hypothetical situation. The Dragonfly Web pages make extensive use of analogous cover stories in the design of interactive decision-making games. Feedback from visitors, patterns of usage, and external reviews provide evidence of effectiveness. A second approach is visual analogies based on the principles of ecological psychology. An empirical example suggests that visual analogies are most effective when there is a one-to-one correspondence between the base and visual target analogs. The use of learner-generated analogies is a third approach. Data from an offline study with undergraduate science students are presented indicating that generating analogies are associated with significant improvements in the ability to place events in natural history on a time line. It is concluded that cyberspace itself might form the basis of the next guiding metaphor of mind.

  3. Unstable Hoogsteen base pairs adjacent to echinomycin binding sites within a DNA duplex

    International Nuclear Information System (INIS)

    Gilbert, D.E.; van der Marel, G.A.; van Boom, J.H.; Feigon, J.

    1989-01-01

    The bisintercalation complex present between the DNA octamer [d(ACGTACGT)] 2 and the cyclic octadepsipeptide antibiotic echinomycin has been studied by one- and two-dimensional proton NMR, and the results obtained have been compared with the crystal structures of related DNA-echinomycin complexes. Two echinomycins are found to bind cooperatively to each DNA duplex at the CpG steps, with the two quinoxaline rings of each echinomycin bisintercalating between the C·G and A·T base pairs. At low temperatures, the A·T base pairs on either side of the intercalation site adopt the Hoogsteen conformation, as observed in the crystal structures. However, as the temperature is raised, the Hoogsteen base pairs in the interior of the duplex are destabilized and are observed to be exchanging between the Hoogsteen base pair and either an open or a Watson-Crick base-paired state. The terminal A·T base pairs, which are not as constrained by the helix as the internal base pairs, remain stably Hoogsteen base-paired up to at least 45 degree C. The implications of these results for the biological role of Hoogsteen base pairs in echinomycin-DNA complexes in vivo are discussed

  4. FRET microscopy autologous tumor lysate processing in mature dendritic cell vaccine therapy

    Directory of Open Access Journals (Sweden)

    Ridolfi Ruggero

    2010-06-01

    Full Text Available Abstract Background Antigen processing by dendritic cells (DC exposed to specific stimuli has been well characterized in biological studies. Nonetheless, the question of whether autologous whole tumor lysates (as used in clinical trials are similarly processed by these cells has not yet been resolved. Methods In this study, we examined the transfer of peptides from whole tumor lysates to major histocompatibility complex class II molecules (MHC II in mature dendritic cells (mDC from a patient with advanced melanoma. Tumor antigenic peptides-MHC II proximity was revealed by Förster Resonance Energy Transfer (FRET measurements, which effectively extends the application of fluorescence microscopy to the molecular level ( Results We detected significant energy transfer between donor and acceptor-labelled antibodies against HLA-DR at the membrane surface of mDC. FRET data indicated that fluorescent peptide-loaded MHC II molecules start to accumulate on mDC membranes at 16 hr from the maturation stimulus, steeply increasing at 22 hr with sustained higher FRET detected up to 46 hr. Conclusions The results obtained imply that the patient mDC correctly processed the tumor specific antigens and their display on the mDC surface may be effective for several days. These observations support the rationale for immunogenic efficacy of autologous tumor lysates.

  5. Fretting Wear Damage Mechanism of Uranium under Various Atmosphere and Vacuum Conditions

    Directory of Open Access Journals (Sweden)

    Zhengyang Li

    2018-04-01

    Full Text Available A fretting wear experiment with uranium has been performed on a linear reciprocating tribometer with ball-on-disk contact. This study focused on the fretting behavior of the uranium under different atmospheres (Ar, Air (21% O2 + 78% N2, and O2 and vacuum conditions (1.05 and 1 × 10−4 Pa. Evolution of friction was assessed by coefficient of friction (COF and friction-dissipated energy. The oxide of the wear surface was evaluated by Raman spectroscopy. The result shows that fretting wear behavior presents strong atmosphere and vacuum condition dependence. With increasing oxygen content, the COF decreases due to abrasive wear and formation of oxide film. The COF in the oxygen condition is at least 0.335, and it has a maximum wear volume of about 1.48 × 107 μm3. However, the COF in a high vacuum condition is maximum about 1.104, and the wear volume is 1.64 × 106 μm3. The COF in the low vacuum condition is very different: it firstly increased and then decreased rapidly to a steady value. It is caused by slight abrasive wear and the formation of tribofilm after thousands of cycles.

  6. Learning Visualizations by Analogy: Promoting Visual Literacy through Visualization Morphing.

    Science.gov (United States)

    Ruchikachorn, Puripant; Mueller, Klaus

    2015-09-01

    We propose the concept of teaching (and learning) unfamiliar visualizations by analogy, that is, demonstrating an unfamiliar visualization method by linking it to another more familiar one, where the in-betweens are designed to bridge the gap of these two visualizations and explain the difference in a gradual manner. As opposed to a textual description, our morphing explains an unfamiliar visualization through purely visual means. We demonstrate our idea by ways of four visualization pair examples: data table and parallel coordinates, scatterplot matrix and hyperbox, linear chart and spiral chart, and hierarchical pie chart and treemap. The analogy is commutative i.e. any member of the pair can be the unfamiliar visualization. A series of studies showed that this new paradigm can be an effective teaching tool. The participants could understand the unfamiliar visualization methods in all of the four pairs either fully or at least significantly better after they observed or interacted with the transitions from the familiar counterpart. The four examples suggest how helpful visualization pairings be identified and they will hopefully inspire other visualization morphings and associated transition strategies to be identified.

  7. The neuromechanism underlying verbal analogical reasoning of metaphorical relations: an event-related potentials study.

    Science.gov (United States)

    Zhao, Ming; Meng, Huishan; Xu, Zhiyuan; Du, Fenglei; Liu, Tao; Li, Yongxin; Chen, Feiyan

    2011-11-24

    Using event-related potentials (ERPs), this study investigated the neuromechanism underlying verbal analogical reasoning of two different metaphorical relations: attributive metaphor and relational metaphor. The analogical reasoning of attributive metaphor (AM-AR) involves a superficial similarity between analogues, while the analogical reasoning of relational metaphor (RM-AR) requires a structural similarity. Subjects were asked to judge whether one word pair was semantically analogous to another word pair. Results showed that the schema induction stage elicited a greater N400 component at the right anterior scalp for the AM-AR and RM-AR tasks, possibly attributable to semantic processing of metaphorical word pairs. The N400 was then followed by a widely distributed P300 and a late negative component (LNC1) at the left anterior scalp. The P300 was possibly related to the formation of a relational category, while the LNC1 was possibly related to the maintenance of a reasoning cue in working memory. The analogy mapping stage elicited broadly distributed N400 and LNC2, which might indicate the presence of semantic retrieval and analogical transfer. In the answer production stage, all conditions elicited the P2 component due to early stimulus encoding. The largest P2 amplitude was in the RM-AR task. The RM-AR elicited a larger LPC than did the AM-AR, even though the baseline correction was taken as a control for the differential P2 effect. The LPC effect might suggest that relational metaphors involved more integration processing than attributive metaphors. Copyright © 2011 Elsevier B.V. All rights reserved.

  8. Fretting fatigue life estimation using fatigue damage gradient correction factor in various contact configurations

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Dong Hyeon; Cho, Sung-San [Hongik University, Seoul (Korea, Republic of)

    2017-03-15

    A fretting fatigue life estimation method that takes into account the stress gradient effect was developed by the authors [Journal of Mechanical Science and Technology, 28 (2014) 2153-2159]. In the developed method, fatigue damage value at the cracking location is corrected with fatigue damage gradient and the corrected value is compared directly with the plain fatigue data for life estimation. In other words, the correction factor is the ratio of plain fatigue damage to fretting fatigue damage at the same life and a function of fatigue damage gradient. Since reliability of the method was verified only for cylinder-on-flat contact configuration in the previous study, the present study extends application of the method to flat-on-flat contact configurations by developing the correction factor for both the contact configuration. Fretting fatigue experiments were conducted to obtain fatigue life data for various fretting pads. Finite element analyses were conducted to evaluate the Smith-Watson-Topper (SWT) fatigue damage parameter in the cracking region. It is revealed that the SWT parameter in fat-on-flat contact configuration decreases exponentially away from the surface as in cylinder-on-flat contact configuration, and thus the SWT gradient at the surface can be evaluated reliably. Moreover, it is found that decrease in the SWT parameter around the cracking location can be expressed by piecewise exponential curves. If the gradient of SWT at the surface is used as a representative value of SWT gradient, it is impossible to establish functional relationship between the SWT gradient and the correction factor for both the contact configurations although it was possible for cylinder-on-flat contact configuration. However, if weighted average of the SWT gradient values obtained from each exponential curve in the piecewise exponential curve is used as a representative value, the correction factor for both the contact configurations becomes a function of the SWT gradient

  9. [Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?].

    Science.gov (United States)

    Brovarets', O O

    2013-01-01

    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 the Löwdin's G*.C* DNA base pair formed by the mutagenic tautomers can acquire, as the A-T Watson-Crick DNA base pair, four biologically important configurations, namely: Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen. This fact demonstrates rather unexpected role of the tautomerisation of the one of the Watson-Crick DNA base pairs, in particular, via double proton transfer: exactly the G.C-->G*.C* tautomerisation allows to overcome steric hindrances for the implementation of the above mentioned configurations. Geometric, electron-topological and energetic properties of the H-bonds that stabilise the studied pairs, as well as the energetic characteristics of the latters are presented.

  10. Analytical use of multi-protein Fluorescence Resonance Energy Transfer to demonstrate membrane-facilitated interactions within cytokine receptor complexes.

    Science.gov (United States)

    Krause, Christopher D; Izotova, Lara S; Pestka, Sidney

    2013-10-01

    Experiments measuring Fluorescence Resonance Energy Transfer (FRET) between cytokine receptor chains and their associated proteins led to hypotheses describing their organization in intact cells. These interactions occur within a larger protein complex or within a given nano-environment. To illustrate this complexity empirically, we developed a protocol to analyze FRET among more than two fluorescent proteins (multi-FRET). In multi-FRET, we model FRET among more than two fluorophores as the sum of all possible pairwise interactions within the complex. We validated our assumption by demonstrating that FRET among pairs within a fluorescent triplet resembled FRET between each pair measured in the absence of the third fluorophore. FRET between two receptor chains increases with increasing FRET between the ligand-binding chain (e.g., IFN-γR1, IL-10R1 and IFN-λR1) and an acylated fluorescent protein that preferentially resides within subsections of the plasma membrane. The interaction of IL-10R2 with IFN-λR1 or IL-10R1 results in decreased FRET between IL-10R2 and the acylated fluorescent protein. Finally, we analyzed FRET among four fluorescent proteins to demonstrate that as FRET between IFN-γR1 and IFN-γR2 or between IFN-αR1 and IFN-αR2c increases, FRET among other pairs of proteins changes within each complex. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Children's Failure in Analogical Reasoning Tasks: A Problem of Focus of Attention and Information Integration?

    Science.gov (United States)

    Glady, Yannick; French, Robert M; Thibaut, Jean-Pierre

    2017-01-01

    Children's improved performance with age in analogy tasks has been explained by an increase in semantic knowledge of the items and the relations between them or by the development of an increased ability to inhibit irrelevant information. We tested the so-called "unbalanced attentional focus hypothesis" that claims that a failure to choose the "analogical" match can be the result of a difficulty to focus on all the relevant information available. Previous eye-tracking research has suggested, in analogies of the A:B::C:D format, that 5-6 year-olds organize their search around the C item. They focused significantly less than adults on the A:B pair, thereby hindering their discovering the relation(s) between A and B. We hypothesized that inducing them to focus their attention on the A:B pair at the beginning of the trial would affect their performance. In Experiment 1, increasing children's focus on the A:B pair did, indeed, lead to better performance. In contrast, in Experiment 2, focusing their attention on the A:B pair impaired performance when the most salient relation holding between A and B was, in fact, irrelevant for the analogy. By contrast, the obvious-but-irrelevant relation in the A:B pair had no negative effect on performance when no explicit A:B focusing was induced. These results are discussed in terms of the temporal organization of the task and availability of information, and of children's difficulties to disengage from the main goal of the task, when necessary.

  12. Experimental studies of resistance fretting-wear of fuel rods for VVER-1000 and TVS-KVADRAT fuel assemblies

    International Nuclear Information System (INIS)

    Makarov, V.; Afanasiev, A.; Egorov, Yu.; Matvienko, I.

    2015-01-01

    The paper covers the results of the studies performed to justify the wear resistance of fuel rods in contact with the spacer grids of TVS VVER-1000 fuel assembly and TVS-KVADRAT square fuel assembly of Russian design for PWR-900 reactor. The presented results of three testing stages comprise: Testing of mockup fuel rods of VVER TVS fuel assembly for fretting wear under the conditions of the water chemistry of VVER reactor; Testing models of different design embodiments of the fuel rods for VVER TVS fuel assembly for fretting wear in still cold water; Testing mockup fuel rods of TVS-KVADRAT square fuel assembly for PWR reactor for frettingwear under the conditions of PWR water chemistry. The effect of structural and operational factors was determined (amplitudes, fuel rod vibration frequencies, values of cladding-to-spacer grid cell gap for the depth of fuel rod cladding wear etc.), an assessment was made of the threshold values of fuel rod vibration parameters, which, if not exceeded, provide the absence of the fuel rod cladding fretting wear in the fuel rod-to spacer grid contact area. Key words: fretting wear, fuel rod, spacer grid, VVER, PWR (author)

  13. A rapid, ratiometric, enzyme-free, and sensitive single-step miRNA detection using three-way junction based FRET probes

    Science.gov (United States)

    Luo, Qingying; Liu, Lin; Yang, Cai; Yuan, Jing; Feng, Hongtao; Chen, Yan; Zhao, Peng; Yu, Zhiqiang; Jin, Zongwen

    2018-03-01

    MicroRNAs (miRNAs) are single stranded endogenous molecules composed of only 18-24 nucleotides which are critical for gene expression regulating the translation of messenger RNAs. Conventional methods based on enzyme-assisted nucleic acid amplification techniques have many problems, such as easy contamination, high cost, susceptibility to false amplification, and tendency to have sequence mismatches. Here we report a rapid, ratiometric, enzyme-free, sensitive, and highly selective single-step miRNA detection using three-way junction assembled (or self-assembled) FRET probes. The developed strategy can be operated within the linear range from subnanomolar to hundred nanomolar concentrations of miRNAs. In comparison with the traditional approaches, our method showed high sensitivity for the miRNA detection and extreme selectivity for the efficient discrimination of single-base mismatches. The results reveal that the strategy paved a new avenue for the design of novel highly specific probes applicable in diagnostics and potentially in microscopic imaging of miRNAs in real biological environments.

  14. Simulation of FRET dyes allows quantitative comparison against experimental data

    Science.gov (United States)

    Reinartz, Ines; Sinner, Claude; Nettels, Daniel; Stucki-Buchli, Brigitte; Stockmar, Florian; Panek, Pawel T.; Jacob, Christoph R.; Nienhaus, Gerd Ulrich; Schuler, Benjamin; Schug, Alexander

    2018-03-01

    Fully understanding biomolecular function requires detailed insight into the systems' structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.

  15. Fretting wear of steam generator tubes: high-temperature tests on AECL rig

    International Nuclear Information System (INIS)

    Guerout, F.; Zbinden, M.

    1993-07-01

    The R and DD has undertaken the study of fretting-wear of Alloy 600 S.G. tubes which occurs by contact with migrating items. The test series was performed in Canada at AECL Research (Atomic Energy of Canada Limited) as part of an exchange program. Four types of configuration were envisaged: a tube-to-drilled hole support contact which provides reference results and three types of tube-to-support contacts which simulate the tube fretting-wear induced by a welding rod, a threaded rod and a knife-edge rod support. This programme is completed by the study of the contact between a S.G. tube and a neighbouring S.G. tube which has been broken after plugging. (authors). 1 tab., 3 refs

  16. Hybridized plasmon in an asymmetric cut-wire-pair structure

    Energy Technology Data Exchange (ETDEWEB)

    Tung, Nguyen Thanh [Vietnamese Military Academy of Science and Technology, Hanoi (Viet Nam); Hanyang University, Seoul (Korea, Republic of); Rhee, Joo Yull [Sungkyunkwan University, Suwon (Korea, Republic of); Park, Jin Woo; Lee, Young Pak [Hanyang University, Seoul (Korea, Republic of)

    2010-12-15

    In this report, we discuss an electromagnetic analog of the molecular-orbital theory for metamaterial structures. We show that the electromagnetic responses of a metamagnetic structure consisting of paired cut-wires can be well understood by using the plasmon-hybridization mechanism. The simulated transmission spectra of the asymmetric cut-wire-pair structure, which were obtained utilizing the transfer-matrix method, strongly support our suggestion.

  17. Accuracy of maximum likelihood estimates of a two-state model in single-molecule FRET

    Energy Technology Data Exchange (ETDEWEB)

    Gopich, Irina V. [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 (United States)

    2015-01-21

    Photon sequences from single-molecule Förster resonance energy transfer (FRET) experiments can be analyzed using a maximum likelihood method. Parameters of the underlying kinetic model (FRET efficiencies of the states and transition rates between conformational states) are obtained by maximizing the appropriate likelihood function. In addition, the errors (uncertainties) of the extracted parameters can be obtained from the curvature of the likelihood function at the maximum. We study the standard deviations of the parameters of a two-state model obtained from photon sequences with recorded colors and arrival times. The standard deviations can be obtained analytically in a special case when the FRET efficiencies of the states are 0 and 1 and in the limiting cases of fast and slow conformational dynamics. These results are compared with the results of numerical simulations. The accuracy and, therefore, the ability to predict model parameters depend on how fast the transition rates are compared to the photon count rate. In the limit of slow transitions, the key parameters that determine the accuracy are the number of transitions between the states and the number of independent photon sequences. In the fast transition limit, the accuracy is determined by the small fraction of photons that are correlated with their neighbors. The relative standard deviation of the relaxation rate has a “chevron” shape as a function of the transition rate in the log-log scale. The location of the minimum of this function dramatically depends on how well the FRET efficiencies of the states are separated.

  18. cAMP biosensors applied in molecular pharmacological studies of G protein-coupled receptors

    DEFF Research Database (Denmark)

    Mathiesen, Jesper Mosolff; Vedel, Line; Bräuner-Osborne, Hans

    2013-01-01

    end-point assays for quantifying GPCR-mediated changes in intracellular cAMP levels exist. More recently, fluorescence resonance energy transfer (FRET)-based cAMP biosensors that can quantify intracellular cAMP levels in real time have been developed. These FRET-based cAMP biosensors have been used...... primarily in single cell FRET microscopy to monitor and visualize changes in cAMP upon GPCR activation. Here, a similar cAMP biosensor with a more efficient mCerulean/mCitrine FRET pair is described for use in the 384-well plate format. After cloning and expression in HEK293 cells, the biosensor...... is characterized in the 384-well plate format and used for measuring the signaling of the G(s)-coupled ß(2)-adrenergic receptor. The procedures described may be applied for other FRET-based biosensors in terms of characterization and conversion to the 384-well plate format....

  19. Intrinsically Labeled Fluorescent Oligonucleotide Probes on Quantum Dots for Transduction of Nucleic Acid Hybridization.

    Science.gov (United States)

    Shahmuradyan, Anna; Krull, Ulrich J

    2016-03-15

    Quantum dots (QDs) have been widely used in chemical and biosensing due to their unique photoelectrical properties and are well suited as donors in fluorescence resonance energy transfer (FRET). Selective hybridization interactions of oligonucleotides on QDs have been determined by FRET. Typically, the QD-FRET constructs have made use of labeled targets or have implemented labeled sandwich format assays to introduce dyes in proximity to the QDs for the FRET process. The intention of this new work is to explore a method to incorporate the acceptor dye into the probe molecule. Thiazole orange (TO) derivatives are fluorescent intercalating dyes that have been used for detection of double-stranded nucleic acids. One such dye system has been reported in which single-stranded oligonucleotide probes were doubly labeled with adjacent thiazole orange derivatives. In the absence of the fully complementary (FC) oligonucleotide target, the dyes form an H-aggregate, which results in quenching of fluorescence emission due to excitonic interactions between the dyes. The hybridization of the FC target to the probe provides for dissociation of the aggregate as the dyes intercalate into the double stranded duplex, resulting in increased fluorescence. This work reports investigation of the dependence of the ratiometric signal on the type of linkage used to conjugate the dyes to the probe, the location of the dye along the length of the probe, and the distance between adjacent dye molecules. The limit of detection for 34mer and 90mer targets was found to be identical and was 10 nM (2 pmol), similar to analogous QD-FRET using labeled oligonucleotide target. The detection system could discriminate a one base pair mismatch (1BPM) target and was functional without substantial compromise of the signal in 75% serum. The 1BPM was found to reduce background signal, indicating that the structure of the mismatch affected the environment of the intercalating dyes.

  20. Analogical reasoning for reliability analysis based on generic data

    Energy Technology Data Exchange (ETDEWEB)

    Kozin, Igor O

    1996-10-01

    The paper suggests using the systemic concept 'analogy' for the foundation of an approach to analyze system reliability on the basis of generic data, describing the method of structuring the set that defines analogical models, an approach of transition from the analogical model to a reliability model and a way of obtaining reliability intervals of analogous objects.

  1. Analogical reasoning for reliability analysis based on generic data

    International Nuclear Information System (INIS)

    Kozin, Igor O.

    1996-01-01

    The paper suggests using the systemic concept 'analogy' for the foundation of an approach to analyze system reliability on the basis of generic data, describing the method of structuring the set that defines analogical models, an approach of transition from the analogical model to a reliability model and a way of obtaining reliability intervals of analogous objects

  2. DNA nanosensor based on biocompatible graphene quantum dots and carbon nanotubes.

    Science.gov (United States)

    Qian, Zhao Sheng; Shan, Xiao Yue; Chai, Lu Jing; Ma, Juan Juan; Chen, Jian Rong; Feng, Hui

    2014-10-15

    An ultrasensitive nanosensor based on fluorescence resonance energy transfer (FRET) between biocompatible graphene quantum dots and carbon nanotubes for DNA detection was reported. We take advantage of good biocompatibility and strong fluorescence of graphene quantum dots, base pairing specificity of DNA and unique fluorescence resonance energy transfer between graphene quantum dots and carbon nanotubes to achieve the analysis of low concentrations of DNA. Graphene quantum dots with high quantum yield up to 0.20 were prepared and served as the fluorophore of DNA probe. FRET process between graphene quantum dots-labeled probe and oxidized carbon nanotubes is easily achieved due to their efficient self-assembly through specific π-π interaction. This nanosensor can distinguish complementary and mismatched nucleic acid sequences with high sensitivity and good reproducibility. The detection method based on this nanosensor possesses a broad linear span of up to 133.0 nM and ultralow detection limit of 0.4 nM. The constructed nanosensor is expected to be highly biocompatible because of all its components with excellent biocompatibility. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Luminescence resonance energy transfer-based nucleic acid hybridization assay on cellulose paper with upconverting phosphor as donors.

    Science.gov (United States)

    Zhou, Feng; Noor, M Omair; Krull, Ulrich J

    2014-03-04

    A bioassay based on DNA hybridization on cellulose paper is a promising format for gene fragment detection that may be suited for in-field and rapid diagnostic applications. We demonstrate for the first time that luminescence resonance energy transfer (LRET) associated with upconverting phosphors (UCPs) can be used to develop a paper-based DNA hybridization assay with high sensitivity, selectivity and fast response. UCPs with strong green emission were synthesized and subsequently functionalized with streptavidin (UCP-strep). UCP-strep particles were immobilized on cellulose paper, and then biotinylated single-stranded oligonucleotide probes were conjugated onto the UCPs via streptavidin-biotin linkage. The UCPs served as donors that were LRET-paired with Cy3-labeled target DNA. Selective DNA hybridization enabled the proximity required for LRET-sensitized emission from Cy3, which was used as the detection signal. Hybridization was complete within 2 min, and the limit of detection of the method was 34 fmol, which is a significant improvement in comparison to an analogous fluorescence resonance energy transfer (FRET) assay based on quantum dots. The assay exhibited excellent resistance to nonspecific adsorption of noncomplementary short/long DNA and protein. The selectivity of the assay was further evaluated by one base pair mismatched (1BPM) DNA detection, where a maximum signal ratio of 3.1:1 was achieved between fully complementary and 1BPM samples. This work represents a preliminary but significant step for the development of paper-based UCP-LRET nucleic acid hybridization assays, which offer potential for lowering the limit of detection of luminescent hybridization assays due to the negligible background signal associated with optical excitation by near-infrared (NIR) light.

  4. A homogeneous fluorometric assay platform based on novel synthetic proteins

    International Nuclear Information System (INIS)

    Vardar-Schara, Goenuel; Krab, Ivo M.; Yi, Guohua; Su, Wei Wen

    2007-01-01

    Novel synthetic recombinant sensor proteins have been created to detect analytes in solution, in a rapid single-step 'mix and read' noncompetitive homogeneous assay process, based on modulating the Foerster resonance energy transfer (FRET) property of the sensor proteins upon binding to their targets. The sensor proteins comprise a protein scaffold that incorporates a specific target-capturing element, sandwiched by genetic fusion between two molecules that form a FRET pair. The utility of the sensor proteins was demonstrated via three examples, for detecting an anti-biotin Fab antibody, a His-tagged recombinant protein, and an anti-FLAG peptide antibody, respectively, all done directly in solution. The diversity of sensor-target interactions that we have demonstrated in this study points to a potentially universal applicability of the biosensing concept. The possibilities for integrating a variety of target-capturing elements with a common sensor scaffold predict a broad range of practical applications

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

    International Nuclear Information System (INIS)

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

    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 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.

  6. Are all analogies created equal? Prefrontal cortical functioning may predict types of analogical reasoning.

    Science.gov (United States)

    Chrysikou, Evangelia G; Thompson-Schill, Sharon L

    2010-06-01

    Abstract The proposed theory can account for analogies based on learned relationships between elements in the source and target domains. However, its explanatory power regarding the discovery of new relationships during analogical reasoning is limited. We offer an alternative perspective for the role of PFC in analogical thought that may better address different types of analogical mappings.

  7. Image magnification based on similarity analogy

    International Nuclear Information System (INIS)

    Chen Zuoping; Ye Zhenglin; Wang Shuxun; Peng Guohua

    2009-01-01

    Aiming at the high time complexity of the decoding phase in the traditional image enlargement methods based on fractal coding, a novel image magnification algorithm is proposed in this paper, which has the advantage of iteration-free decoding, by using the similarity analogy between an image and its zoom-out and zoom-in. A new pixel selection technique is also presented to further improve the performance of the proposed method. Furthermore, by combining some existing fractal zooming techniques, an efficient image magnification algorithm is obtained, which can provides the image quality as good as the state of the art while greatly decrease the time complexity of the decoding phase.

  8. The synergy of corrosion and fretting wear process on Inconel 690 in the high temperature high pressure water environment

    Science.gov (United States)

    Wang, Zihao; Xu, Jian; Li, Jie; Xin, Long; Lu, Yonghao; Shoji, Tetsuo; Takeda, Yoichi; Otsuka, Yuichi; Mutoh, Yoshiharu

    2018-04-01

    The synergistic effect of corrosion and fretting process of the steam generator (SG) tube was investigated by using a self-designed high temperature test rig in this paper. The experiments were performed at 100°C , 200°C and 288°C , respectively. The fretting corrosion damage was studied by optical microscopy (OM), scanning electron microscope (SEM), energy dispersive spectrometer (EDS), Raman spectroscopy and auger electron spectroscopy (AES). The results demonstrated that the corrosion process in high temperature high pressure (HTHP) water environment had a distinct interaction with the fretting process of Inconel 690. With the increment of temperature, the damage mechanism changed from a simple mechanical process to a mechanochemical process.

  9. A Novel Analog Integrated Circuit Design Course Covering Design, Layout, and Resulting Chip Measurement

    Science.gov (United States)

    Lin, Wei-Liang; Cheng, Wang-Chuan; Wu, Chen-Hao; Wu, Hai-Ming; Wu, Chang-Yu; Ho, Kuan-Hsuan; Chan, Chueh-An

    2010-01-01

    This work describes a novel, first-year graduate-level analog integrated circuit (IC) design course. The course teaches students analog circuit design; an external manufacturer then produces their designs in three different silicon chips. The students, working in pairs, then test these chips to verify their success. All work is completed within…

  10. Determination of cDNA encoding BCR/ABL fusion gene in patients with chronic myelogenous leukemia using a novel FRET-based quantum dots-DNA nanosensor.

    Science.gov (United States)

    Shamsipur, Mojtaba; Nasirian, Vahid; Barati, Ali; Mansouri, Kamran; Vaisi-Raygani, Asad; Kashanian, Soheila

    2017-05-08

    In the present study, we developed a sensitive method based on fluorescence resonance energy transfer (FRET) for the determination of the BCR/ABL fusion gene, which is used as a biomarker to confirm the clinical diagnosis of both chronic myelogenous leukemia (CML) and acute lymphocytic leukemia (ALL). For this purpose, CdTe quantum dots (QDs) were conjugated to amino-modified 18-mer oligonucleotide ((N)DNA) to form the QDs-(N)DNA nanosensor. In the presence of methylene blue (MB) as an intercalator, the hybridization of QDs-(N)DNA with the target BCR/ABL fusion gene (complementary DNA), brings the MB (acceptor) at close proximity of the QDs (donor), leading to FRET upon photoexcitation of the QDs. The enhancement in the emission intensity of MB was used to follow up the hybridization, which was linearly proportional to concentration of the target complementary DNA in a range from 1.0 × 10 -9 to 1.25 × 10 -7  M. The detection limit of the proposed method was obtained to be 1.5 × 10 -10  M. Finally, the feasibility and selectivity of the proposed nanosensor was evaluated by the analysis of derived nucleotides from both mismatched sequences and clinical samples of patients with leukemia as real samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Prévision de l'épaisseur du film passif d'un acier inoxydable 316L soumis au fretting corrosion grâce au Point Defect Model, PDM Predicting the steady state thickness of passive films with the Point Defect Model in fretting corrosion experiments

    Directory of Open Access Journals (Sweden)

    Geringer Jean

    2013-11-01

    . This passive layer of few nanometers, at ambient temperature, is the key of our civilization according to some authors. This work is dedicated to predict the passive layer thicknesses of stainless steel under fretting corrosion with a specific emphasis on the role of proteins. The model is based on the Point Defect Model (micro scale and an update of the model on the friction process (micro-macro scale. Genetic algorithm was used for finding solution of the problem. The major results are, as expected from experimental results, albumin prevents from degradation at the lowest concentration of chlorides; an incubation time is necessary for degrading the passive film; under fretting corrosion and high concentration of chlorides the passive behavior is annihilated.

  12. Paper-based solid-phase nucleic acid hybridization assay using immobilized quantum dots as donors in fluorescence resonance energy transfer.

    Science.gov (United States)

    Noor, M Omair; Shahmuradyan, Anna; Krull, Ulrich J

    2013-02-05

    A paper-based solid-phase assay is presented for transduction of nucleic acid hybridization using immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). The surface of paper was modified with imidazole groups to immobilize QD-probe oligonucleotide conjugates that were assembled in solution. Green-emitting QDs (gQDs) were FRET-paired with Cy3 acceptor. Hybridization of Cy3-labeled oligonucleotide targets provided the proximity required for FRET-sensitized emission from Cy3, which served as an analytical signal. The assay exhibited rapid transduction of nucleic acid hybridization within minutes. Without any amplification steps, the limit of detection of the assay was found to be 300 fmol with the upper limit of the dynamic range at 5 pmol. The implementation of glutathione-coated QDs for the development of nucleic acid hybridization assay integrated on a paper-based platform exhibited excellent resistance to nonspecific adsorption of oligonucleotides and showed no reduction in the performance of the assay in the presence of large quantities of noncomplementary DNA. The selectivity of nucleic acid hybridization was demonstrated by single-nucleotide polymorphism (SNP) detection at a contrast ratio of 19 to 1. The reuse of paper over multiple cycles of hybridization and dehybridization was possible, with less than 20% reduction in the performance of the assay in five cycles. This work provides an important framework for the development of paper-based solid-phase QD-FRET nucleic acid hybridization assays that make use of a ratiometric approach for detection and analysis.

  13. Extracting rate coefficients from single-molecule photon trajectories and FRET efficiency histograms for a fast-folding protein.

    Science.gov (United States)

    Chung, Hoi Sung; Gopich, Irina V; McHale, Kevin; Cellmer, Troy; Louis, John M; Eaton, William A

    2011-04-28

    Recently developed statistical methods by Gopich and Szabo were used to extract folding and unfolding rate coefficients from single-molecule Förster resonance energy transfer (FRET) data for proteins with kinetics too fast to measure waiting time distributions. Two types of experiments and two different analyses were performed. In one experiment bursts of photons were collected from donor and acceptor fluorophores attached to a 73-residue protein, α(3)D, freely diffusing through the illuminated volume of a confocal microscope system. In the second, the protein was immobilized by linkage to a surface, and photons were collected until one of the fluorophores bleached. Folding and unfolding rate coefficients and mean FRET efficiencies for the folded and unfolded subpopulations were obtained from a photon by photon analysis of the trajectories using a maximum likelihood method. The ability of the method to describe the data in terms of a two-state model was checked by recoloring the photon trajectories with the extracted parameters and comparing the calculated FRET efficiency histograms with the measured histograms. The sum of the rate coefficients for the two-state model agreed to within 30% with the relaxation rate obtained from the decay of the donor-acceptor cross-correlation function, confirming the high accuracy of the method. Interestingly, apparently reliable rate coefficients could be extracted using the maximum likelihood method, even at low (rate coefficients and mean FRET efficiencies were also obtained in an approximate procedure by simply fitting the FRET efficiency histograms, calculated by binning the donor and acceptor photons, with a sum of three-Gaussian functions. The kinetics are exposed in these histograms by the growth of a FRET efficiency peak at values intermediate between the folded and unfolded peaks as the bin size increases, a phenomenon with similarities to NMR exchange broadening. When comparable populations of folded and unfolded

  14. The Effect of Modulation Ratio of Cu/Ni Multilayer Films on the Fretting Damage Behaviour of Ti-811 Titanium Alloy.

    Science.gov (United States)

    Zhang, Xiaohua; Liu, Daoxin; Li, Xiaoying; Dong, Hanshan; Xi, Yuntao

    2017-05-26

    To improve the fretting damage (fretting wear and fretting fatigue) resistance of Ti-811 titanium alloy, three Cu/Ni multilayer films with the same modulation period thickness (200 nm) and different modulation ratios (3:1, 1:1, 1:3) were deposited on the surface of the alloy via ion-assisted magnetron sputtering deposition (IAD). The bonding strength, micro-hardness, and toughness of the films were evaluated, and the effect of the modulation ratio on the room-temperature fretting wear (FW) and fretting fatigue (FF) resistance of the alloy was determined. The results indicated that the IAD technique can be successfully used to prepare Cu/Ni multilayer films, with high bonding strength, low-friction, and good toughness, which yield improved room-temperature FF and FW resistance of the alloy. For the same modulation period (200 nm), the micro-hardness, friction, and FW resistance of the coated alloy increased, decreased, and improved, respectively, with increasing modulation ratio of the Ni-to-Cu layer thickness. However, the FF resistance of the coated alloy increased non-monotonically with the increasing modulation ratio. Among the three Cu/Ni multilayer films, those with a modulation ratio of 1:1 can confer the highest FF resistance to the Ti-811 alloy, owing mainly to their unique combination of good toughness, high strength, and low-friction.

  15. Fretting wear of Inconel 625 at high temperature and in high vacuum

    International Nuclear Information System (INIS)

    Iwabuchi, A.

    1985-01-01

    The purpose of this work was to investigate the fretting properties of Inconel 625 at high temperature and in high vacuum. Experiments were carried out under constant conditions with a normal load of 14 N and a peak-to-peak slip amplitude of 110 μm and through 6x10 4 cycles. Several environmental conditions were used. Pressure was varied between 10 -3 and 10 5 Pa at temperatures of 20 and 500 0 C. Temperatures up to 500 0 C were also used at pressures of 10 -3 and 10 5 Pa. At 10 -3 Pa and 500 0 C wear loss was negligible but wear scars showed severe damage consisting of deep cracks and accretion of transferred debris. The coefficient of friction then maintained a high value of 1.7 throughout the fretting test. The critical pressure below which oxidation rate becomes reduced is 10 Pa, a value independent of temperature. At pressures below this critical value the coefficient of friction increases steeply and the fretting mechanism changes from one of oxidative wear to one of adhesive wear. A compacted so-called 'glaze' oxide was formed at temperatures above 300 0 C in air (10 5 Pa) and at pressures above 10 3 Pa at 500 0 C. A comparison of results for Inconel 625 with those for S45C and SUS304 steels and Inconel 600 is given. (orig.)

  16. Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma.

    Science.gov (United States)

    Hirao, Ichiro; Kimoto, Michiko

    2012-01-01

    Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A-T and G-C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating "proof of concept" experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.

  17. Paper-based solid-phase multiplexed nucleic acid hybridization assay with tunable dynamic range using immobilized quantum dots as donors in fluorescence resonance energy transfer.

    Science.gov (United States)

    Noor, M Omair; Krull, Ulrich J

    2013-08-06

    A multiplexed solid-phase nucleic acid hybridization assay on a paper-based platform is presented using multicolor immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). The surface of paper was modified with imidazole groups to immobilize two types of QD-probe oligonucleotide conjugates that were assembled in solution. Green-emitting QDs (gQDs) and red-emitting QDs (rQDs) served as donors with Cy3 and Alexa Fluor 647 (A647) acceptors. The gQD/Cy3 FRET pair served as an internal standard, while the rQD/A647 FRET pair served as a detection channel, combining the control and analytical test zones in one physical location. Hybridization of dye-labeled oligonucleotide targets provided the proximity for FRET sensitized emission from the acceptor dyes, which served as an analytical signal. Hybridization assays in the multicolor format provided a limit of detection of 90 fmol and an upper limit of dynamic range of 3.5 pmol. The use of an array of detection zones was designed to provide improved analytical figures of merit compared to that which could be achieved on one type of array design in terms of relative concentration of multicolor QDs. The hybridization assays showed excellent resistance to nonspecific adsorption of oligonucleotides. Selectivity of the two-plex hybridization assay was demonstrated by single nucleotide polymorphism (SNP) detection at a contrast ratio of 50:1. Additionally, it is shown that the use of preformed QD-probe oligonucleotide conjugates and consideration of the relative number density of the two types of QD-probe conjugates in the two-color assay format is advantageous to maximize assay sensitivity and the upper limit of dynamic range.

  18. Covering All the Bases in Genetics: Simple Shorthands and Diagrams for Teaching Base Pairing to Biology Undergraduates

    Directory of Open Access Journals (Sweden)

    Sergei Kuchin

    2011-03-01

    Full Text Available Explaining base pairing is an important element in teaching undergraduate genetics. I propose a teaching approach that aims to close the gap between the mantra “A pairs with T, and G pairs with C” and the “intimidating” chemical diagrams. The approach offers a set of simple “shorthands” for the key bases that can be used to quickly deduce all canonical and wobble pairs that the students need to know. The approach can be further developed to analyze mutagenic mismatch pairing.

  19. Homo-FRET Imaging as a tool to quantify protein and lipid clustering

    NARCIS (Netherlands)

    Bader, A.N.; Hoetzl, S.; Hofman, E.G.; Voortman, J.; van Bergen en Henegouwen, P.M.P.; van Meer, G.; Gerritsen, H.C.

    2010-01-01

    Homo-FRET, Förster resonance energy transfer between identical fluorophores, can be conveniently measured by observing its effect on the fluorescence anisotropy. This review aims to summarize the possibilities of fluorescence anisotropy imaging techniques to investigate clustering of identical

  20. CdSe/ZnS quantum dots conjugated with a fluorescein derivative: a FRET-based pH sensor for physiological alkaline conditions.

    Science.gov (United States)

    Kurabayashi, Tomokazu; Funaki, Nayuta; Fukuda, Takeshi; Akiyama, Shinnosuke; Suzuki, Miho

    2014-01-01

    Dual pH-dependent fluorescence peaks from a semiconductor quantum dot (QD) and a pH-dependent fluorescent dye can be measured by irradiating with a single wavelength light, and the pH can be estimated from the ratio of the fluorescent intensity of the two peaks. In this work, ratiometric pH sensing was achieved in an aqueous environment by a fluorescent CdSe/ZnS QD appended with a pH-sensitive organic dye, based on fluorescence resonance energy transfer (FRET). By functionalizing the CdSe/ZnS QD with 5-(and 6)-carboxynaphthofluorescein succinimidyl ester as a pH-dependent fluorescent dye, we succeeded in fabricating sensitive nanocomplexes with a linear response to a broad range of physiological pH levels (7.5-9.5) when excited at 450 nm. We found that a purification process is important for increasing the high-fluorescence intensity ratio of a ratiometric fluorescence pH-sensor, and the fluorescence intensity ratio was improved up to 1.0 at pH 8.0 after the purification process to remove unreacted CdSe/ZnS QDs even though the fluorescence of the dye could not be observed without the purification process. The fluorescence intensity ratio corresponds to the fluorescence intensity of the dye, and this fluorescent dye exhibited pH-dependent fluorescence intensity changes. These facts indicate that the fluorescence intensity ratio linearly increased with increasing pH value of the buffer solution containing the QD and the dye. The FRET efficiencies changed from 0.3 (pH 7.5) to 6.2 (pH 9.5).

  1. Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.

    Science.gov (United States)

    Fuertes, Gustavo; Banterle, Niccolò; Ruff, Kiersten M; Chowdhury, Aritra; Mercadante, Davide; Koehler, Christine; Kachala, Michael; Estrada Girona, Gemma; Milles, Sigrid; Mishra, Ankur; Onck, Patrick R; Gräter, Frauke; Esteban-Martín, Santiago; Pappu, Rohit V; Svergun, Dmitri I; Lemke, Edward A

    2017-08-01

    Unfolded states of proteins and native states of intrinsically disordered proteins (IDPs) populate heterogeneous conformational ensembles in solution. The average sizes of these heterogeneous systems, quantified by the radius of gyration ( R G ), can be measured by small-angle X-ray scattering (SAXS). Another parameter, the mean dye-to-dye distance ( R E ) for proteins with fluorescently labeled termini, can be estimated using single-molecule Förster resonance energy transfer (smFRET). A number of studies have reported inconsistencies in inferences drawn from the two sets of measurements for the dimensions of unfolded proteins and IDPs in the absence of chemical denaturants. These differences are typically attributed to the influence of fluorescent labels used in smFRET and to the impact of high concentrations and averaging features of SAXS. By measuring the dimensions of a collection of labeled and unlabeled polypeptides using smFRET and SAXS, we directly assessed the contributions of dyes to the experimental values R G and R E For chemically denatured proteins we obtain mutual consistency in our inferences based on R G and R E , whereas for IDPs under native conditions, we find substantial deviations. Using computations, we show that discrepant inferences are neither due to methodological shortcomings of specific measurements nor due to artifacts of dyes. Instead, our analysis suggests that chemical heterogeneity in heteropolymeric systems leads to a decoupling between R E and R G that is amplified in the absence of denaturants. Therefore, joint assessments of R G and R E combined with measurements of polymer shapes should provide a consistent and complete picture of the underlying ensembles.

  2. Optimizing FRET-FLIM Labeling Conditions to Detect Nuclear Protein Interactions at Native Expression Levels in Living Arabidopsis Roots

    KAUST Repository

    Long, Yuchen

    2018-05-15

    Protein complex formation has been extensively studied using Förster resonance energy transfer (FRET) measured by Fluorescence Lifetime Imaging Microscopy (FLIM). However, implementing this technology to detect protein interactions in living multicellular organism at single-cell resolution and under native condition is still difficult to achieve. Here we describe the optimization of the labeling conditions to detect FRET-FLIM in living plants. This study exemplifies optimization procedure involving the identification of the optimal position for the labels either at the N or C terminal region and the selection of the bright and suitable, fluorescent proteins as donor and acceptor labels for the FRET study. With an effective optimization strategy, we were able to detect the interaction between the stem cell regulators SHORT-ROOT and SCARECROW at endogenous expression levels in the root pole of living Arabidopsis embryos and developing lateral roots by FRET-FLIM. Using this approach we show that the spatial profile of interaction between two transcription factors can be highly modulated in reoccurring and structurally resembling organs, thus providing new information on the dynamic redistribution of nuclear protein complex configurations in different developmental stages. In principle, our optimization procedure for transcription factor complexes is applicable to any biological system.

  3. Fretting wear behavior of zirconium alloy in B-Li water at 300 °C

    Science.gov (United States)

    Zhang, Lefu; Lai, Ping; Liu, Qingdong; Zeng, Qifeng; Lu, Junqiang; Guo, Xianglong

    2018-02-01

    The tangential fretting wear of three kinds of zirconium alloys tube mated with 304 stainless steel (SS) plate was investigated. The tests were conducted in an autoclave containing 300 °C pressurized B-Li water for tube-on-plate contact configuration. The worn surfaces were examined with scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and 3D microscopy. The cross-section of wear scar was examined with transmission electron microscope (TEM). The results indicated that the dominant wear mechanism of zirconium alloys in this test condition was delamination and oxidation. The oxide layer on the fretted area consists of outer oxide layer composed of iron oxide and zirconium oxide and inner oxide layer composed of zirconium oxide.

  4. Advanced non-linear flow-induced vibration and fretting-wear analysis capabilities

    Energy Technology Data Exchange (ETDEWEB)

    Toorani, M.; Pan, L.; Li, R.; Idvorian, N. [Babcock and Wilcox Canada Ltd., Cambridge, Ontario (Canada); Vincent, B.

    2009-07-01

    Fretting wear is a potentially significant degradation mechanism in nuclear steam generators and other shell and tube heat transfer equipment as well. This paper presents an overview of the recently developed code FIVDYNA which is used for the non-linear flow-induced vibration and fretting wear analysis for operating steam generators (OTSG and RSG) and shell-and-tube heat exchangers. FIVDYNA is a non-linear time-history Flow-Induced Vibration (FIV) analysis computer program that has been developed by Babcock and Wilcox Canada to advance the understanding of tube vibration and tube to tube-support interaction. In addition to the dynamic fluid induced forces the program takes into account other tube static forces due to axial and lateral tube preload and thermal interaction loads. The program is capable of predicting the location where the fretting wear is most likely to occur and its magnitude taking into account the support geometry including gaps. FIVDYNA uses the general purpose finite element computer code ABAQUS as its solver. Using ABAQUS gives the user the flexibility to add additional forces to the tube ranging from tube preloads and the support offsets to thermal loads. The forces currently being modeled in FIVDYNA are the random turbulence, steady drag force, fluid-elastic forces, support offset and pre-strain force (axial loads). This program models the vibration of tubes and calculates the structural dynamic characteristics, and interaction forces between the tube and the tube supports. These interaction forces are then used to calculate the work rate at the support and eventually the predicted depth of wear scar on the tube. A very good agreement is found with experiments and also other computer codes. (author)

  5. A Comparative Study on the Formation Mechanism of Wear Scars during the Partial and Full Scale Fretting Wear Tests of Spacer Grids

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young Ho; Shin, Chang Hwan; Oh, Dong Seok; Kang, Heung Seok [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-05-15

    Fretting wear studies for evaluating the contact damages of nuclear fuel rods have been focused on the contact shape, rod motion, contact condition, environment, etc.. However, fretting wear mechanism was dramatically changed with slight variation of test variables such as test environments and contact shapes. For example, in an unlubricated condition, effects of wear debris and/or its layer on the fretting wear mechanism showed that the formation of a well-developed layer on the contact surfaces has a beneficial effect for decreasing a friction coefficient. Otherwise, a severe wear was happened due to a third body abrasion. In addition, in water lubrication condition, some of wear debris was remained on worn surface of fuel rod specimens at both sliding and impacting loading conditions. So, it is apparent that a wear rate of fuel rod specimen was easily accelerated by the third-body abrasion. This is because the restrained agglomeration behavior between generated wear particles results in rapid removal of wear debris and its layer. In case of contact shape effects, previous studies show that wear debris are easily trapped between contact surfaces and its debris layer was well developed in a localized area especially in a concave spring rather than a convex spring shape. Consequently, localized wear was happened at both ends of a concave spring and center region of a convex spring. So, it is useful for determining the fretting wear resistance of spacer gird spring and dimple by using part unit in the various lubricated conditions. It is well known that the fretting wear phenomenon of nuclear fuel rod is originated from a flow-induced vibration (FIV) due to the rapid primary coolant. This means that both rod vibration and debris removal behavior were affected by flow fields around the contact regions between fuel rod and spring/dimple. However, all most of the fretting tests were performed by simulating rod vibrating motions such as axial vibration, conservative rod

  6. A Comparative Study on the Formation Mechanism of Wear Scars during the Partial and Full Scale Fretting Wear Tests of Spacer Grids

    International Nuclear Information System (INIS)

    Lee, Young Ho; Shin, Chang Hwan; Oh, Dong Seok; Kang, Heung Seok

    2012-01-01

    Fretting wear studies for evaluating the contact damages of nuclear fuel rods have been focused on the contact shape, rod motion, contact condition, environment, etc.. However, fretting wear mechanism was dramatically changed with slight variation of test variables such as test environments and contact shapes. For example, in an unlubricated condition, effects of wear debris and/or its layer on the fretting wear mechanism showed that the formation of a well-developed layer on the contact surfaces has a beneficial effect for decreasing a friction coefficient. Otherwise, a severe wear was happened due to a third body abrasion. In addition, in water lubrication condition, some of wear debris was remained on worn surface of fuel rod specimens at both sliding and impacting loading conditions. So, it is apparent that a wear rate of fuel rod specimen was easily accelerated by the third-body abrasion. This is because the restrained agglomeration behavior between generated wear particles results in rapid removal of wear debris and its layer. In case of contact shape effects, previous studies show that wear debris are easily trapped between contact surfaces and its debris layer was well developed in a localized area especially in a concave spring rather than a convex spring shape. Consequently, localized wear was happened at both ends of a concave spring and center region of a convex spring. So, it is useful for determining the fretting wear resistance of spacer gird spring and dimple by using part unit in the various lubricated conditions. It is well known that the fretting wear phenomenon of nuclear fuel rod is originated from a flow-induced vibration (FIV) due to the rapid primary coolant. This means that both rod vibration and debris removal behavior were affected by flow fields around the contact regions between fuel rod and spring/dimple. However, all most of the fretting tests were performed by simulating rod vibrating motions such as axial vibration, conservative rod

  7. Eye Movements Reveal Optimal Strategies for Analogical Reasoning.

    Science.gov (United States)

    Vendetti, Michael S; Starr, Ariel; Johnson, Elizabeth L; Modavi, Kiana; Bunge, Silvia A

    2017-01-01

    Analogical reasoning refers to the process of drawing inferences on the basis of the relational similarity between two domains. Although this complex cognitive ability has been the focus of inquiry for many years, most models rely on measures that cannot capture individuals' thought processes moment by moment. In the present study, we used participants' eye movements to investigate reasoning strategies in real time while solving visual propositional analogy problems (A:B::C:D). We included both a semantic and a perceptual lure on every trial to determine how these types of distracting information influence reasoning strategies. Participants spent more time fixating the analogy terms and the target relative to the other response choices, and made more saccades between the A and B items than between any other items. Participants' eyes were initially drawn to perceptual lures when looking at response choices, but they nonetheless performed the task accurately. We used participants' gaze sequences to classify each trial as representing one of three classic analogy problem solving strategies and related strategy usage to analogical reasoning performance. A project-first strategy, in which participants first extrapolate the relation between the AB pair and then generalize that relation for the C item, was both the most commonly used strategy as well as the optimal strategy for solving visual analogy problems. These findings provide new insight into the role of strategic processing in analogical problem solving.

  8. Eye Movements Reveal Optimal Strategies for Analogical Reasoning

    Directory of Open Access Journals (Sweden)

    Michael S. Vendetti

    2017-06-01

    Full Text Available Analogical reasoning refers to the process of drawing inferences on the basis of the relational similarity between two domains. Although this complex cognitive ability has been the focus of inquiry for many years, most models rely on measures that cannot capture individuals' thought processes moment by moment. In the present study, we used participants' eye movements to investigate reasoning strategies in real time while solving visual propositional analogy problems (A:B::C:D. We included both a semantic and a perceptual lure on every trial to determine how these types of distracting information influence reasoning strategies. Participants spent more time fixating the analogy terms and the target relative to the other response choices, and made more saccades between the A and B items than between any other items. Participants' eyes were initially drawn to perceptual lures when looking at response choices, but they nonetheless performed the task accurately. We used participants' gaze sequences to classify each trial as representing one of three classic analogy problem solving strategies and related strategy usage to analogical reasoning performance. A project-first strategy, in which participants first extrapolate the relation between the AB pair and then generalize that relation for the C item, was both the most commonly used strategy as well as the optimal strategy for solving visual analogy problems. These findings provide new insight into the role of strategic processing in analogical problem solving.

  9. Time resolved amplified FRET identifies protein kinase B activation state as a marker for poor prognosis in clear cell renal cell carcinoma

    Directory of Open Access Journals (Sweden)

    James Miles

    2017-12-01

    General significance: The quantitative imaging technology based on Amplified-FRET can rapidly analyse protein activation states and molecular interactions. It could be used for prognosis and assess drug function during the early cycles of chemotherapy. It enables evaluation of clinical efficiency of personalised cancer treatment.

  10. Stability Loss of the Cemented Stem of Hip Prosthesis due to Fretting Corrosion Fatigue

    Directory of Open Access Journals (Sweden)

    L. Capitanu

    2017-12-01

    Full Text Available Aim of this project was to study the fretting behaviour of the cemented femoral stem fixation of a total hip prosthesis, trying to capture the loss of contact between the femoral stem and polymetylmethacrilate cement fixation. To have a landmark, studies were performed compared with cementless fixation, where no fretting phenomenon occurs, on real prostheses, under biological 3D loading conditions. A fatigue test device, installed on a servo-hydraulic triaxial dynamic testing machine was used. It allowed monitoring the flexion-extension, abduction-adduction, inner-outer rotation movements, and the variation of the torsional torque, depending on normal loading. The test ends when the sample does not fail after 2000000 cycles, or when it has reached a predetermined number of cycles. Test fluid medium used was NaCl mixed with distilled water, a favourable environment for appearance of fretting corrosion. After the failure of stem fixation at 2450000 cycles, the mantle of bone cement remaining adherent on femoral stem was removed. Microscopic inspection of the femoral stem and of the inner part of the polymetylmethacrilate mantle demonstrated the existence of corrosion of the femoral stem surface beneath the cement mantle, and Fe2O3 deposits on the femoral stem surface and on the inner part of the mantle.

  11. Steady-state acceptor fluorescence anisotropy imaging under evanescent excitation for visualisation of FRET at the plasma membrane.

    Directory of Open Access Journals (Sweden)

    Viviane Devauges

    Full Text Available We present a novel imaging system combining total internal reflection fluorescence (TIRF microscopy with measurement of steady-state acceptor fluorescence anisotropy in order to perform live cell Förster Resonance Energy Transfer (FRET imaging at the plasma membrane. We compare directly the imaging performance of fluorescence anisotropy resolved TIRF with epifluorescence illumination. The use of high numerical aperture objective for TIRF required correction for induced depolarization factors. This arrangement enabled visualisation of conformational changes of a Raichu-Cdc42 FRET biosensor by measurement of intramolecular FRET between eGFP and mRFP1. Higher activity of the probe was found at the cell plasma membrane compared to intracellularly. Imaging fluorescence anisotropy in TIRF allowed clear differentiation of the Raichu-Cdc42 biosensor from negative control mutants. Finally, inhibition of Cdc42 was imaged dynamically in live cells, where we show temporal changes of the activity of the Raichu-Cdc42 biosensor.

  12. FRET-Aptamer Assays for Bone Marker Assessment, C-Telopeptide, Creatinine, and Vitamin D

    Science.gov (United States)

    Bruno, John G.

    2013-01-01

    Astronauts lose 1.0 to 1.5% of their bone mass per month on long-duration spaceflights. NASA wishes to monitor the bone loss onboard spacecraft to develop nutritional and exercise countermeasures, and make adjustments during long space missions. On Earth, the same technology could be used to monitor osteoporosis and its therapy. Aptamers bind to targets against which they are developed, much like antibodies. However, aptamers do not require animal hosts or cell culture and are therefore easier, faster, and less expensive to produce. In addition, aptamers sometimes exhibit greater affinity and specificity vs. comparable antibodies. In this work, fluorescent dyes and quenchers were added to the aptamers to enable pushbutton, one-step, bind-and-detect fluorescence resonance energy transfer (FRET) assays or tests that can be freeze-dried, rehydrated with body fluids, and used to quantitate bone loss of vitamin D levels with a handheld fluorometer in the spacecraft environment. This work generated specific, rapid, one-step FRET assays for the bone loss marker C-telopeptide (CTx) when extracted from urine, creatinine from urine, and vitamin D congeners in diluted serum. The assays were quantified in nanograms/mL using a handheld fluorometer connected to a laptop computer to convert the raw fluorescence values into concentrations of each analyte according to linear standard curves. DNA aptamers were selected and amplified for several rounds against a 26- amino acid form of CTx, creatinine, and vitamin D. The commonalities between loop structures were studied, and several common loop structures were converted into aptamer beacons with a fluorophore and quencher on each end. In theory, when the aptamer beacon binds its cognate target (CTx bone peptide, creatinine, or vitamin D), it is forced open and no longer quenched, so it gives off fluorescent light (when excited) in proportion to the amount of target present in a sample. This proportional increase in fluorescence is

  13. Determination of Equilibrium Constant and Relative Brightness in FRET-FCS by Including the Third-Order Correlations.

    Science.gov (United States)

    Meng, Lingyi; He, Shanshan; Zhao, Xin Sheng

    2017-12-21

    Fluorescence correlation spectroscopy (FCS) encodes the information on the equilibrium constant (K), the relative fluorescence brightness of fluorophore (Q), and the forward and backward reaction rate constants (k + and k - ) on a physical or chemical relaxation. However, it has been a long-standing problem to completely resolve the FCS data to get the thermodynamic and kinetic information. Recently, we have solved the problem for fluorescence autocorrelation spectroscopy (FACS). Here, we extend the method to fluorescence cross-correlation spectroscopy (FCCS), which appears when FCS is coupled with fluorescence resonance energy transfer (FRET). Among 12 total second-order and third-order pre-exponential factors in a relaxation process probed by the FRET-FCS technique, 3 are independent. We presented and discussed 3 sets of explicit solutions to use these pre-exponential factors to calculate K and Q. Together with the relaxation time, the acquired K will allow people to obtain k + and k - , so that the goal of deciphering the FRET-FCS data will be fully reached. The theory is verified by extensive computer simulations and tested experimentally on a system of oligonucleotide hybridization.

  14. Influence of thermal oxidation duration on the microstructure and fretting wear behavior of Ti6Al4V alloy

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Song [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Department of Mechanical Engineering, Tsinghua University, Beijing 100084 (China); Liao, Zhenhua [Department of Mechanical Engineering, Tsinghua University, Beijing 100084 (China); Biomechanics and Biotechnology Lab, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057 (China); Liu, Yuhong [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Department of Mechanical Engineering, Tsinghua University, Beijing 100084 (China); Liu, Weiqiang, E-mail: weiqliu@hotmail.com [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Biomechanics and Biotechnology Lab, Research Institute of Tsinghua University in Shenzhen, Shenzhen 518057 (China)

    2015-06-01

    Thermal oxidation under water oxidizing atmosphere was performed on Ti6Al4V alloy under different durations from 2 h to 8 h. Surface characterizations were performed using X-ray diffractometery (XRD), scanning electron microscopy (SEM), Raman spectroscopy, nanoindentation and nano scratch testing. Fretting wear behaviors of untreated and oxidized samples were also examined. The formed oxide coating mainly included rutile TiO{sub 2} as well as a little alumina. The weight gain with respect to the oxidation duration obeyed the linear oxidation kinetics law. The growth of oxide grains was in inadequate growth state of incomplete scale coverage from 2nd to 4th hour duration, in normal growth state from 4th to 6th hour duration while in excessive growth state of oxide particle agglomeration and surface roughening from 6th to 8th (or more than 8th) hour duration. The coating thickness increased from 5 μm to 12 μm as oxidation duration increased from 2 h to 8 h. The increase in duration also increased surface roughness and nano hardness as well as adhesion strength of the film/substrate for oxidized samples. The nano hardness value was 10.06 ± 2.15 GPa and the critical load of failure during nano scratch testing was 554.3 ± 6.44 mN for 4 h treated sample. The untreated and oxidized samples showed a same fretting running status and fretting regime with a displacement amplitude of 200 μm while revealing different fretting failure mechanisms. It was mainly abrasive and adhesive wear under ploughing force for untreated sample, while a mix of 3-body abrasion by rolling oxide particles and severe plastic deformation under high contact stress between two ceramic materials for the oxidized samples. The oxide coating was not worn out and improved the fretting wear resistance of titanium alloy. - Highlights: • A thickness of 5–12 μm rutile TiO{sub 2} coating formed under different oxidation durations. • Weight gain with respect to oxidation duration obeyed linear

  15. Analog implementation of an integral resonant control scheme

    International Nuclear Information System (INIS)

    Pereira, E; Moheimani, S O R; Aphale, S S

    2008-01-01

    Integral resonant control (IRC) has been introduced as a high performance controller design methodology for flexible structures with collocated actuator–sensor pairs. IRC has a simple structure and is capable of achieving significant damping, over several modes, while guaranteeing closed-loop stability of the system in the presence of unmodeled out-of-bandwidth dynamics. IRC can be an ideal controller for various industrial damping applications, if packaged in a simple easy-to-implement electronic module. This work proposes an analog implementation of the IRC scheme using a single Op-Amp circuit. The objective is to show that with simple analog realization of the modified IRC scheme, it is possible to damp a large number of vibration modes. A brief discussion about the modeling, circuit considerations, implementation and experimental results is presented in order to validate the usefulness and practicality of the proposed analog IRC implementation. (technical note)

  16. Revisitation of FRET methods to measure intraprotein distances in Human Serum Albumin

    Energy Technology Data Exchange (ETDEWEB)

    Santini, S.; Bizzarri, A.R.; Cannistraro, S., E-mail: cannistr@unitus.it

    2016-11-15

    We revisited the FRET methods to measure the intraprotein distance between Trp-214 (used as donor) of Human Serum Albumin and its Cys-34, labelled with 1.5-Iaedans (used as acceptor). Variation of Trp fluorescence emission in terms of both intensity and lifetime, as well the enhancement of the acceptor fluorescence emission upon Trp excitation, have been monitored. A careful statistical analysis of the fluorescence results from ten independently prepared samples, combined with suitable spectral corrections, provided reproducible distances estimations by each one of the three methods. Even if monitoring of the donor lifetime variation in the presence of the acceptor reproduces at the best the crystallographic data, by allowing even sub-nanometre distance variations to be appreciated, we suggest that a comparative analysis of all the three methods, applied with statistical significance, should be preferred to achieve a better reliability of the FRET technique.

  17. Uzawa algorithm to solve elastic and elastic-plastic fretting wear problems within the bipotential framework

    Science.gov (United States)

    Ning, Po; Feng, Zhi-Qiang; Quintero, Juan Antonio Rojas; Zhou, Yang-Jing; Peng, Lei

    2018-03-01

    This paper deals with elastic and elastic-plastic fretting problems. The wear gap is taken into account along with the initial contact distance to obtain the Signorini conditions. Both the Signorini conditions and the Coulomb friction laws are written in a compact form. Within the bipotential framework, an augmented Lagrangian method is applied to calculate the contact forces. The Archard wear law is then used to calculate the wear gap at the contact surface. The local fretting problems are solved via the Uzawa algorithm. Numerical examples are performed to show the efficiency and accuracy of the proposed approach. The influence of plasticity has been discussed.

  18. Dichotomy Boundary at Aeolis Mensae, Mars: Fretted Terrain Developed in a Sedimentary Deposit

    Science.gov (United States)

    Irwin, R. P., III; Watters, T. R.; Howard, A. D.; Maxwell, T. A.; Craddock, R. A.

    2003-03-01

    Fretted terrain in Aeolis Mensae, Mars, developed in a sedimentary deposit. A thick, massive unit with a capping layer or duricrust overlies a more durable layered sequence. Wind, collapse, and minor fluvial activity contributed to degradation.

  19. What works with worked examples: Extending self-explanation and analogical comparison to synthesis problems

    Science.gov (United States)

    Badeau, Ryan; White, Daniel R.; Ibrahim, Bashirah; Ding, Lin; Heckler, Andrew F.

    2017-12-01

    The ability to solve physics problems that require multiple concepts from across the physics curriculum—"synthesis" problems—is often a goal of physics instruction. Three experiments were designed to evaluate the effectiveness of two instructional methods employing worked examples on student performance with synthesis problems; these instructional techniques, analogical comparison and self-explanation, have previously been studied primarily in the context of single-concept problems. Across three experiments with students from introductory calculus-based physics courses, both self-explanation and certain kinds of analogical comparison of worked examples significantly improved student performance on a target synthesis problem, with distinct improvements in recognition of the relevant concepts. More specifically, analogical comparison significantly improved student performance when the comparisons were invoked between worked synthesis examples. In contrast, similar comparisons between corresponding pairs of worked single-concept examples did not significantly improve performance. On a more complicated synthesis problem, self-explanation was significantly more effective than analogical comparison, potentially due to differences in how successfully students encoded the full structure of the worked examples. Finally, we find that the two techniques can be combined for additional benefit, with the trade-off of slightly more time on task.

  20. Fluorescence-based characterization of genetically encoded peptides that fold in live cells: progress toward a generic hairpin scaffold

    Science.gov (United States)

    Cheng, Zihao; Campbell, Robert E.

    2007-02-01

    Binding proteins suitable for expression and high affinity molecular recognition in the cytoplasm or nucleus of live cells have numerous applications in the biological sciences. In an effort to add a new minimal motif to the growing repertoire of validated non-immunoglobulin binding proteins, we have undertaken the development of a generic protein scaffold based on a single β-hairpin that can fold efficiently in the cytoplasm. We have developed a method, based on the measurement of fluorescence resonance energy transfer (FRET) between a genetically fused cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP), that allows the structural stability of recombinant β-hairpin peptides to be rapidly assessed both in vitro and in vivo. We have previously reported the validation of this method when applied to a 16mer tryptophan zipper β-hairpin. We now describe the use of this method to evaluate the potential of a designed 20mer β-hairpin peptide with a 3rd Trp/Trp cross-strand pair to function as a generic protein scaffold. Quantitative analysis of the FRET efficiency, resistance to proteolysis (assayed by loss of FRET), and circular dichroism spectra revealed that the 20mer peptide is significantly more tolerant of destabilizing mutations than the 16mer peptide. Furthermore, we experimentally demonstrate that the in vitro determined β-hairpin stabilities are well correlated with in vivo β-hairpin stabilities as determined by FRET measurements of colonies of live bacteria expressing the recombinant peptides flanked by CFP and YFP. Finally, we report on our progress to develop highly folded 24mer and 28mer β-hairpin peptides through the use of fluorescence-based library screening.

  1. FRET based integrated pyrene-AgNPs system for detection of Hg (II) and pyrene dimer: Applications to environmental analysis

    Science.gov (United States)

    Walekar, Laxman S.; Hu, Peidong; Vafaei Molamahmood, Hamed; Long, Mingce

    2018-06-01

    The integrated system of pyrene and cetyltrimethyl ammonium bromide (CTAB) capped silver nanoparticles (AgNPs) with a distance (r) of 2.78 nm has been developed for the detection of Hg (II) and pyrene dimer. The interaction between pyrene and AgNPs results in the fluorescence quenching of pyrene due to the energy transfer, whose mechanism can be attributed to the Forster Resonance Energy Transfer (FRET) supported by experimental observation and theoretical calculations. The developed probe shows a highly selective and sensitive response towards Hg (II) probably due to the amalgam formation, which results in the fluorescence recovery (90%) of pyrene and color change of solution from yellowish brown to colorless. The addition of Hg (II) may increase the distance between pyrene and AgNPs undergoes the 'FRET OFF' process. This system gives a selective response towards Hg (II) over other competing metal ions. Under the optimal condition, the system offers good linearity between 0.1 and 0.6 μg mL-1 with a detection limit of 62 ng mL-1. In addition, the system also provides an effective platform for detection of pyrene in its dimer form even at very low concentrations (10 ng mL-1) on the surface of AgNPs. Therefore, it could be used as effective alternatives for the detection of Hg (II) as well as pyrene simultaneously.

  2. Signature scheme based on bilinear pairs

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  4. Expectation-maximization of the potential of mean force and diffusion coefficient in Langevin dynamics from single molecule FRET data photon by photon.

    Science.gov (United States)

    Haas, Kevin R; Yang, Haw; Chu, Jhih-Wei

    2013-12-12

    The dynamics of a protein along a well-defined coordinate can be formally projected onto the form of an overdamped Lagevin equation. Here, we present a comprehensive statistical-learning framework for simultaneously quantifying the deterministic force (the potential of mean force, PMF) and the stochastic force (characterized by the diffusion coefficient, D) from single-molecule Förster-type resonance energy transfer (smFRET) experiments. The likelihood functional of the Langevin parameters, PMF and D, is expressed by a path integral of the latent smFRET distance that follows Langevin dynamics and realized by the donor and the acceptor photon emissions. The solution is made possible by an eigen decomposition of the time-symmetrized form of the corresponding Fokker-Planck equation coupled with photon statistics. To extract the Langevin parameters from photon arrival time data, we advance the expectation-maximization algorithm in statistical learning, originally developed for and mostly used in discrete-state systems, to a general form in the continuous space that allows for a variational calculus on the continuous PMF function. We also introduce the regularization of the solution space in this Bayesian inference based on a maximum trajectory-entropy principle. We use a highly nontrivial example with realistically simulated smFRET data to illustrate the application of this new method.

  5. A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A.

    Science.gov (United States)

    Sobieraj, M; Krzyśko, K A; Jarmuła, A; Kalinowski, M W; Lesyng, B; Prokopowicz, M; Cieśla, J; Gojdź, A; Kierdaszuk, B

    2015-04-01

    Predicting FRET pathways in proteins using computer simulation techniques is very important for reliable interpretation of experimental data. A novel and relatively simple methodology has been developed and applied to purine nucleoside phosphorylase (PNP) complexed with a fluorescent ligand - formycin A (FA). FRET occurs between an excited Tyr residue (D*) and FA (A). This study aims to interpret experimental data that, among others, suggests the absence of FRET for the PNPF159A mutant in complex with FA, based on novel theoretical methodology. MD simulations for the protein molecule containing D*, and complexed with A, are carried out. Interactions of D* with its molecular environment are accounted by including changes of the ESP charges in S1, compared to S0, and computed at the SCF-CI level. FRET probability W F depends on the inverse six-power of the D*-A distance, R da . The orientational factor 0 < k(2) < 4 between D* and A is computed and included in the analysis. Finally W F is time-averaged over the MD trajectories resulting in its mean value. The red-shift of the tyrosinate anion emission and thus lack of spectral overlap integral and thermal energy dissipation are the reasons for the FRET absence in the studied mutants at pH 7 and above. The presence of the tyrosinate anion results in a competitive energy dissipation channel and red-shifted emission, thus in consequence in the absence of FRET. These studies also indicate an important role of the phenyl ring of Phe159 for FRET in the wild-type PNP, which does not exist in the Ala159 mutant, and for the effective association of PNP with FA. In a more general context, our observations point out very interesting and biologically important properties of the tyrosine residue in its excited state, which may undergo spontaneous deprotonation in the biomolecular systems, resulting further in unexpected physical and/or biological phenomena. Until now, this observation has not been widely discussed in the

  6. A combined experimental and finite element approach to analyse the fretting mechanism of the head-stem taper junction in total hip replacement

    NARCIS (Netherlands)

    Bitter, T.; Khan, I.; Marriott, T.; Lovelady, E.; Verdonschot, N.J.; Janssen, D.W.

    2017-01-01

    Fretting corrosion at the taper interface of modular hip implants has been implicated as a possible cause of implant failure. This study was set up to gain more insight in the taper mechanics that lead to fretting corrosion. The objectives of this study therefore were (1) to select experimental

  7. Accurate interaction energies of base pairing and base stacking. The final chapter

    Czech Academy of Sciences Publication Activity Database

    Šponer, Jiří; Jurečka, Petr; Hobza, Pavel

    2005-01-01

    Roč. 22, č. 6 (2005), s. 767 ISSN 0739-1102. [Albany 2005. Conversation /14./. 14.06.2005-18.06.2005, Albany] Institutional research plan: CEZ:AV0Z50040507 Keywords : base pairing * base stacking * nucleic acids Subject RIV: BO - Biophysics

  8. NASA Software Cost Estimation Model: An Analogy Based Estimation Model

    Science.gov (United States)

    Hihn, Jairus; Juster, Leora; Menzies, Tim; Mathew, George; Johnson, James

    2015-01-01

    The cost estimation of software development activities is increasingly critical for large scale integrated projects such as those at DOD and NASA especially as the software systems become larger and more complex. As an example MSL (Mars Scientific Laboratory) developed at the Jet Propulsion Laboratory launched with over 2 million lines of code making it the largest robotic spacecraft ever flown (Based on the size of the software). Software development activities are also notorious for their cost growth, with NASA flight software averaging over 50% cost growth. All across the agency, estimators and analysts are increasingly being tasked to develop reliable cost estimates in support of program planning and execution. While there has been extensive work on improving parametric methods there is very little focus on the use of models based on analogy and clustering algorithms. In this paper we summarize our findings on effort/cost model estimation and model development based on ten years of software effort estimation research using data mining and machine learning methods to develop estimation models based on analogy and clustering. The NASA Software Cost Model performance is evaluated by comparing it to COCOMO II, linear regression, and K-­ nearest neighbor prediction model performance on the same data set.

  9. Correlative FRET: new method improves rigor and reproducibility in determining distances within synaptic nanoscale architecture

    Science.gov (United States)

    Shinogle-Decker, Heather; Martinez-Rivera, Noraida; O'Brien, John; Powell, Richard D.; Joshi, Vishwas N.; Connell, Samuel; Rosa-Molinar, Eduardo

    2018-02-01

    A new correlative Förster Resonance Energy Transfer (FRET) microscopy method using FluoroNanogold™, a fluorescent immunoprobe with a covalently attached Nanogold® particle (1.4nm Au), overcomes resolution limitations in determining distances within synaptic nanoscale architecture. FRET by acceptor photobleaching has long been used as a method to increase fluorescence resolution. The transfer of energy from a donor to an acceptor generally occurs between 10-100Å, which is the relative distance between the donor molecule and the acceptor molecule. For the correlative FRET microscopy method using FluoroNanogold™, we immuno-labeled GFP-tagged-HeLa-expressing Connexin 35 (Cx35) with anti-GFP and with anti-Cx35/36 antibodies, and then photo-bleached the Cx before processing the sample for electron microscopic imaging. Preliminary studies reveal the use of Alexa Fluor® 594 FluoroNanogold™ slightly increases FRET distance to 70Å, in contrast to the 62.5Å using AlexaFluor 594®. Preliminary studies also show that using a FluoroNanogold™ probe inhibits photobleaching. After one photobleaching session, Alexa Fluor 594® fluorescence dropped to 19% of its original fluorescence; in contrast, after one photobleaching session, Alexa Fluor 594® FluoroNanogold™ fluorescence dropped to 53% of its original intensity. This result confirms that Alexa Fluor 594® FluoroNanogold™ is a much better donor probe than is Alexa Fluor 594®. The new method (a) creates a double confirmation method in determining structure and orientation of synaptic architecture, (b) allows development of a two-dimensional in vitro model to be used for precise testing of multiple parameters, and (c) increases throughput. Future work will include development of FluoroNanogold™ probes with different sizes of gold for additional correlative microscopy studies.

  10. A Study on Corrosion and Fretting Wear Resistance of Alloy 690 Tubes

    Energy Technology Data Exchange (ETDEWEB)

    Won, Ju Jin; Min, Su Jung; Kim, Myeong Su; Kim, Kyu Tae [Dongguk Univ., Gyeongju (Korea, Republic of)

    2013-10-15

    In this article, the effects of such failures have on the materials of alloy 690 are assessed. The corroded volume variation and mass decreased continuously with time. However, the oxide volume changes in an irregular pattern since the oxide formed on the alloy 690 metal may be detached due to the flake formation. The amount of the fretting wear increased with time. It can be seen that the wear rate increased with time and reduced at the later time. The test results show that the ductility decreased as corrosion increases. Alloy 690 is broadly used as a material of nuclear power plant's steam generator tubes because of its excellent mechanical strength, corrosion properties, wear properties and stability at a high temperature. However, the tubes for nuclear power plant's steam generators become a major threat for lifetime management and efficient operation of nuclear power plant due to various corrosion and fretting wear failures caused by flow-induced vibration (FIV) that occurs between tubes.

  11. Medical diagnosis and remote sensing at fiber-tip: picosecond resolved FRET sensor

    Science.gov (United States)

    Polley, Nabarun; Pal, Samir Kumar

    2016-03-01

    Förster Resonance Energy Transfer (FRET) strategy in popular in fiber-optic sensing. However, the steady state emission quenching of the donor is inadequate to conclude FRET. The resonance type energy transfer from one molecule (donor) to other (acceptor) should meet few key properties including donor to acceptor energy migration in non-radiative way. In the present study, we have coupled the evanescent field of an optical fiber to the covalently attached donor (dansyl) molecules at the fiber tip. By using picosecond resolved time correlated single photon counting (TCSPC) we have demonstrated that dansyl at the fiber tip transfers energy to a well known DNA-intercalating dye ethidium. Our ultrafast detection scheme selectively distinguishes the probe (dansyl) emission from the intrinsic emission of the fiber. We have also used the setup for the remote sensing of the dielectric constant (polarity) of an environment. We have finally implemented the detection mechanism to detect an industrial synthetic dye methylene blue (MB) in water.

  12. AudioPairBank: Towards A Large-Scale Tag-Pair-Based Audio Content Analysis

    OpenAIRE

    Sager, Sebastian; Elizalde, Benjamin; Borth, Damian; Schulze, Christian; Raj, Bhiksha; Lane, Ian

    2016-01-01

    Recently, sound recognition has been used to identify sounds, such as car and river. However, sounds have nuances that may be better described by adjective-noun pairs such as slow car, and verb-noun pairs such as flying insects, which are under explored. Therefore, in this work we investigate the relation between audio content and both adjective-noun pairs and verb-noun pairs. Due to the lack of datasets with these kinds of annotations, we collected and processed the AudioPairBank corpus cons...

  13. Förster Resonance Energy Transfer (FRET as a Tool for Dissecting the Molecular Mechanisms for Maturation of the Shigella Type III Secretion Needle Tip Complex

    Directory of Open Access Journals (Sweden)

    William D. Picking

    2012-11-01

    Full Text Available Förster resonance energy transfer (FRET provides a powerful tool for monitoring intermolecular interactions and a sensitive technique for studying Å-level protein conformational changes. One system that has particularly benefited from the sensitivity and diversity of FRET measurements is the maturation of the Shigella type III secretion apparatus (T3SA needle tip complex. The Shigella T3SA delivers effector proteins into intestinal cells to promote bacterial invasion and spread. The T3SA is comprised of a basal body that spans the bacterial envelope and a needle with an exposed tip complex that matures in response to environmental stimuli. FRET measurements demonstrated bile salt binding by the nascent needle tip protein IpaD and also mapped resulting structural changes which led to the recruitment of the translocator IpaB. At the needle tip IpaB acts as a sensor for host cell contact but prior to secretion, it is stored as a heterodimeric complex with the chaperone IpgC. FRET analyses showed that chaperone binding to IpaB’s N-terminal domain causes a conformational change in the latter. These FRET analyses, with other biophysical methods, have been central to understanding T3SA maturation and will be highlighted, focusing on the details of the FRET measurements and the relevance to this particular system.

  14. Analog fourier transform channelizer and OFDM receiver

    OpenAIRE

    2007-01-01

    An OFDM receiver having an analog multiplier based I-Q channelizing filter, samples and holds consecutive analog I-Q samples of an I-Q baseband, the I-Q basebands having OFDM sub-channels. A lattice of analog I-Q multipliers and analog I-Q summers concurrently receives the held analog I-Q samples, performs analog I-Q multiplications and analog I-Q additions to concurrently generate a plurality of analog I-Q output signals, representing an N-point discrete Fourier transform of the held analog ...

  15. Eye movements provide insight into individual differences in children's analogical reasoning strategies.

    Science.gov (United States)

    Starr, Ariel; Vendetti, Michael S; Bunge, Silvia A

    2018-05-01

    Analogical reasoning is considered a key driver of cognitive development and is a strong predictor of academic achievement. However, it is difficult for young children, who are prone to focusing on perceptual and semantic similarities among items rather than relational commonalities. For example, in a classic A:B::C:? propositional analogy task, children must inhibit attention towards items that are visually or semantically similar to C, and instead focus on finding a relational match to the A:B pair. Competing theories of reasoning development attribute improvements in children's performance to gains in either executive functioning or semantic knowledge. Here, we sought to identify key drivers of the development of analogical reasoning ability by using eye gaze patterns to infer problem-solving strategies used by six-year-old children and adults. Children had a greater tendency than adults to focus on the immediate task goal and constrain their search based on the C item. However, large individual differences existed within children, and more successful reasoners were able to maintain the broader goal in mind and constrain their search by initially focusing on the A:B pair before turning to C and the response choices. When children adopted this strategy, their attention was drawn more readily to the correct response option. Individual differences in children's reasoning ability were also related to rule-guided behavior but not to semantic knowledge. These findings suggest that both developmental improvements and individual differences in performance are driven by the use of more efficient reasoning strategies regarding which information is prioritized from the start, rather than the ability to disengage from attractive lure items. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Advances in Spiropyrans/Spirooxazines and Applications Based on Fluorescence Resonance Energy Transfer (FRET with Fluorescent Materials

    Directory of Open Access Journals (Sweden)

    Hongyan Xia

    2017-12-01

    Full Text Available Studies on the following were reviewed: (1 the structure of spiropyrans and spirooxazines (two kinds of spiro compounds under external stimuli and (2 the construction and applications of composite systems based on fluorescence resonance energy transfer (FRET with fluorescent materials. When treated with different stimuli (light, acids and bases, solvents, metal ions, temperature, redox potential, and so on, spiropyrans/spirooxazines undergo transformations between the ring-closed form (SP, the ring-opened merocyanine (MC form, and the protonated ring-opened form (MCH. This is due to the breakage of the spiro C–O bond and the protonation of MC, along with a color change. Various novel, multifunctional materials based on photochromic spiropyrans and spirooxazines have been successfully developed because of the vastly differently physiochemical properties posssed by the SP, MC and MCH forms. Among the three different structural forms, the MC form has been studied most extensively. The MC form not only gives complexes with various inorganic particles, biological molecules, and organic chemicals but also acts as the energy acceptor (of energy from fluorescent molecules during energy transfer processes that take place under proper conditions. Furthermore, spiropyran and spirooxazine compounds exhibit reversible physicochemical property changes under proper stimuli; this provides more advantages compared with other photochromic compounds. Additionally, the molecular structures of spiropyrans and spirooxazines can be easily modified and extended, so better compounds can be obtained to expand the scope of already known applications. Described in detail are: (1 the structural properties of spiropyrans and spirooxazines and related photochromic mechanisms; (2 composite systems based on spiropyrans and spirooxazines, and (3 fluorescent materials which have potential applications in sensing, probing, and a variety of optical elements.

  17. Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

    Science.gov (United States)

    Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

    2018-05-01

    In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

  18. Inductive, Analogical, and Communicative Generalization

    Directory of Open Access Journals (Sweden)

    Adri Smaling

    2003-03-01

    Full Text Available Three forms of inductive generalization - statistical generalization, variation-based generalization and theory-carried generalization - are insufficient concerning case-to-case generalization, which is a form of analogical generalization. The quality of case-to-case generalization needs to be reinforced by setting up explicit analogical argumentation. To evaluate analogical argumentation six criteria are discussed. Good analogical reasoning is an indispensable support to forms of communicative generalization - receptive and responsive (participative generalization — as well as exemplary generalization.

  19. Advances in Analog Circuit Design 2015

    CERN Document Server

    Baschirotto, Andrea; Harpe, Pieter

    2016-01-01

    This book is based on the 18 tutorials presented during the 24th workshop on Advances in Analog Circuit Design. Expert designers present readers with information about a variety of topics at the frontier of analog circuit design, including low-power and energy-efficient analog electronics, with specific contributions focusing on the design of efficient sensor interfaces and low-power RF systems. This book serves as a valuable reference to the state-of-the-art, for anyone involved in analog circuit research and development. ·         Provides a state-of-the-art reference in analog circuit design, written by experts from industry and academia; ·         Presents material in a tutorial-based format; ·         Includes coverage of high-performance analog-to-digital and digital to analog converters, integrated circuit design in scaled technologies, and time-domain signal processing.

  20. DFT study on metal-mediated uracil base pair complexes

    Directory of Open Access Journals (Sweden)

    Ayhan Üngördü

    2017-11-01

    Full Text Available The most stable of metal-mediated uracil base pair complexes were determined. Method was used density functional theory, B3LYP. The calculations of systems containing C, H, N, O were described by 6-311++G(d,p and cc-PVTZ basis sets and LANL2DZ and SDD basis sets was used for transition metals. Then Egap values of complexes were calculated and the electrical conductivity of the complexes for single nanowires was studied by band theory. Metal-mediated uracil base pair complexes which will be used as conductive wires in nanotechnology were predicted. In nanoworld, this study is expected to show a way for practical applications.

  1. Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair

    KAUST Repository

    Chawla, Mohit

    2018-01-02

    The fluorescent non-natural 4-aminophthalimide (4AP) base, when paired to the complementary 2,4-diaminopyrimidine (DAP) nucleobase, is accommodated in a B-DNA duplex being efficiently recognized and incorporated by DNA polymerases. To complement the experimental studies and rationalize the impact of the above non-natural bases on the structure, stability and dynamics of nucleic acid structures, we performed quantum mechanics (QM) calculations along with classical molecular dynamics (MD) simulations. QM calculations were initially focused on the geometry and energetics of the 4AP:DAP non-natural pair and of H-bonded base pairs between 4AP and all the natural bases in their classical Watson-Crick geometries. The QM calculations indicate that the 4AP:DAP pair, despite the fact that it can form 3 H-bonds in a classic Watson-Crick geometry, has a stability comparable to the A:T pair. Then, we extended the study to reverse Watson-Crick geometries, characteristic of parallel strands. MD simulations were carried out on two 13-mer DNA duplexes, featuring a central 4AP:DAP or A:T pair, respectively. No major structural deformation of the duplex was observed during the MD simulation. Snapshots from the MD simulations were subjected to QM calculations to investigate the 4AP:DAP interaction energy when embedded into a duplex structure, and to investigate the impact of the two non-natural bases on the stacking interactions with adjacent bases in the DNA duplex. We found a slight increase in stacking interactions involving the 4AP:DAP pair, counterbalanced by a moderate decrease in H-bonding interactions of the 4AP:DAP and of the adjacent base pairs in the duplex. The results of our study are in agreement with experimental data and complement them by providing an insight into which factors contribute positively and which factors contribute negatively to the structural compatibility of the fluorescent 4AP:DAP pair with a B-DNA structure.

  2. Assessment of fretting wear in Hanaro fuel

    International Nuclear Information System (INIS)

    Chae, Hee Taek; Lim, Kyeong Hwan; Kim, Hark Rho

    1999-06-01

    Since the first fuel loading on Feb. 1995, various zero-power tests were performed in HANARO and power ascending tests followed. After the initial fuel loading, Hanaro operation staffs inspected only two fuel bundles which were evaluated to have the highest power at the end of each cycle and they did not recognize anything peculiar in the inspected bundles. At the end of 1996, Hanaro staffs found severe wear damages in the fuel components. After that, the 4th cycle core was re-arranged with fresh fuels only to investigate wear phenomena on the fuel components. The fuel inspections have been performed 25 times periodically since the core re-configuration. In this report, fretting wear characteristics of the fuel assemblies were evaluated and summarized. Wear damages of the improved fuel assembly to resolve the wear problem were compared with those of the original fuel assembly. Based on the results of the fuel inspections, we suggest that fuel inspection need not be done for the first 60 pump operation days in order to reduce the potential of damage by a fuel handling error and an operator's burden of the fuel inspection. (author). 6 refs., 10 tabs., 5 figs

  3. Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes

    Directory of Open Access Journals (Sweden)

    David Llères

    2017-02-01

    Full Text Available How metazoan genomes are structured at the nanoscale in living cells and tissues remains unknown. Here, we adapted a quantitative FRET (Förster resonance energy transfer-based fluorescence lifetime imaging microscopy (FLIM approach to assay nanoscale chromatin compaction in living organisms. Caenorhabditis elegans was chosen as a model system. By measuring FRET between histone-tagged fluorescent proteins, we visualized distinct chromosomal regions and quantified the different levels of nanoscale compaction in meiotic cells. Using RNAi and repetitive extrachromosomal array approaches, we defined the heterochromatin state and showed that its architecture presents a nanoscale-compacted organization controlled by Heterochromatin Protein-1 (HP1 and SETDB1 H3-lysine-9 methyltransferase homologs in vivo. Next, we functionally explored condensin complexes. We found that condensin I and condensin II are essential for heterochromatin compaction and that condensin I additionally controls lowly compacted regions. Our data show that, in living animals, nanoscale chromatin compaction is controlled not only by histone modifiers and readers but also by condensin complexes.

  4. Can nanophotonics control the Förster resonance energy transfer efficiency?

    DEFF Research Database (Denmark)

    Blum, C.; Zijlstra, N.; Lagendijk, A.

    2013-01-01

    from photovoltaics and lighting, to probing molecular distances and interactions.It is an intriguing open question whether the FRET rate γFRET and the energy transfer efficiency ηFRET can also be controlled by the nanoscale optical environment, characterized by the local density of optical states (LDOS...... precisely-defined, isolated, and efficient donor-acceptor pairs. The FRET pairs are dye molecules that covalently bound to the opposite ends of a 15 basepair long double-stranded with a precisely defined distance of 6.8 nm. Control over the LDOS is realized by positioning the FRET systems at well...... of the energy donor by the LDOS, the energy transfer efficiency can be enhanced or reduced. If a donor with unit quantum efficiency is placed in a 3D photonic bandgap, the energy transfer efficiency will approach 100 %, independent of the acceptor, and of the distances and orientations between the FRET partners....

  5. Children’s Failure in Analogical Reasoning Tasks: A Problem of Focus of Attention and Information Integration?

    Directory of Open Access Journals (Sweden)

    Yannick Glady

    2017-05-01

    Full Text Available Children’s improved performance with age in analogy tasks has been explained by an increase in semantic knowledge of the items and the relations between them or by the development of an increased ability to inhibit irrelevant information. We tested the so-called “unbalanced attentional focus hypothesis” that claims that a failure to choose the “analogical” match can be the result of a difficulty to focus on all the relevant information available. Previous eye-tracking research has suggested, in analogies of the A:B::C:D format, that 5–6 year-olds organize their search around the C item. They focused significantly less than adults on the A:B pair, thereby hindering their discovering the relation(s between A and B. We hypothesized that inducing them to focus their attention on the A:B pair at the beginning of the trial would affect their performance. In Experiment 1, increasing children’s focus on the A:B pair did, indeed, lead to better performance. In contrast, in Experiment 2, focusing their attention on the A:B pair impaired performance when the most salient relation holding between A and B was, in fact, irrelevant for the analogy. By contrast, the obvious-but-irrelevant relation in the A:B pair had no negative effect on performance when no explicit A:B focusing was induced. These results are discussed in terms of the temporal organization of the task and availability of information, and of children’s difficulties to disengage from the main goal of the task, when necessary.

  6. Children’s Failure in Analogical Reasoning Tasks: A Problem of Focus of Attention and Information Integration?

    Science.gov (United States)

    Glady, Yannick; French, Robert M.; Thibaut, Jean-Pierre

    2017-01-01

    Children’s improved performance with age in analogy tasks has been explained by an increase in semantic knowledge of the items and the relations between them or by the development of an increased ability to inhibit irrelevant information. We tested the so-called “unbalanced attentional focus hypothesis” that claims that a failure to choose the “analogical” match can be the result of a difficulty to focus on all the relevant information available. Previous eye-tracking research has suggested, in analogies of the A:B::C:D format, that 5–6 year-olds organize their search around the C item. They focused significantly less than adults on the A:B pair, thereby hindering their discovering the relation(s) between A and B. We hypothesized that inducing them to focus their attention on the A:B pair at the beginning of the trial would affect their performance. In Experiment 1, increasing children’s focus on the A:B pair did, indeed, lead to better performance. In contrast, in Experiment 2, focusing their attention on the A:B pair impaired performance when the most salient relation holding between A and B was, in fact, irrelevant for the analogy. By contrast, the obvious-but-irrelevant relation in the A:B pair had no negative effect on performance when no explicit A:B focusing was induced. These results are discussed in terms of the temporal organization of the task and availability of information, and of children’s difficulties to disengage from the main goal of the task, when necessary. PMID:28588516

  7. An N=2 dual pair and a phase transition

    International Nuclear Information System (INIS)

    Aspinwall, P.S.

    1996-01-01

    We carefully analyze the N=2 dual pair of string theories in four dimensions introduced by Ferrara, Harvey, Strominger and Vafa. The analysis shows that a second discrete degree of freedom must be switched on in addition to the known ''Wilson line'' to achieve a non-perturbatively consistent theory. We also identify the phase transition this model undergoes into another dual pair via a process analogous to a conifold transition. This provides the first known example of a phase transition which is understood from both the type II and the heterotic string picture. (orig.)

  8. A homogeneous assay for highly sensitive detection of CaMV35S promoter in transgenic soybean by förster resonance energy transfer between nitrogen-doped graphene quantum dots and Ag nanoparticles

    International Nuclear Information System (INIS)

    Li, Yaqi; Sun, Li; Qian, Jing; Wang, Chengke; Liu, Qian; Han, En; Hao, Nan; Zhang, Liuping; Cai, Jianrong; Wang, Kun

    2016-01-01

    In this work, a novel homogeneous assay for DNA quantitative analysis based on förster resonance energy transfer (FRET) was developed for cauliflwer mosaic virus 35s (CaMV35S) promoter of transgenic soybean detection. The homogenous FRET of fluorescence signal was fabricated by DNA hybridization with probe modified nitrogen-doped graphene quantum dots (NGQDs) and silver nanoparticles (AgNPs), which acted the donor-acceptor pairs for the first time. The highly efficient FRET and unique properties of the NGQDs made the proposed FRET system as a functionalized detection platform for labelling of DNA. Upon the recognition of specific target DNA (tDNA), the FRET between NGQDs and AgNPs was triggered to produce fluorescence quenching, which could be used for tDNA detection. The fabricated homogeneous FRET assay displayed a wide linear range of 0.1–500.0 nM and a low limit of detection 0.03 nM for the detection of CaMV35S (S/N = 3). This proposed biosensor revealed high specificity to detect tDNA, with acceptable intra-assay precision and excellent stability. This method was successfully applied to identify the real sample of 0.5% containing transgenic soybean, which achieved the most of national law regulations. This assay was further validated by polymerase chain reaction as the genetically modified organisms, suggesting that the proposed FRET system is a feasible tool for the further daily genetically modified organism detection. - Highlights: • Both NGQDs and AgNPs were selected as the novel FRET donor-acceptor pairs. • The proposed homogeneous FRET assay was developed for CaMV35S detection. • The resulting method could identify 0.5% containing transgenic soybean sample. • This assay was inexpensive, simple and highly sensitive.

  9. A homogeneous assay for highly sensitive detection of CaMV35S promoter in transgenic soybean by förster resonance energy transfer between nitrogen-doped graphene quantum dots and Ag nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yaqi; Sun, Li [School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013 (China); Qian, Jing [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013 (China); Wang, Chengke [School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013 (China); Liu, Qian [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013 (China); Han, En [School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013 (China); Hao, Nan [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013 (China); Zhang, Liuping [Sinograin Zhenjiang Grains & Oils Quality Testing Center Co., Ltd., Zhenjiang, 212013 (China); Cai, Jianrong, E-mail: jrcai@ujs.edu.cn [School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013 (China); Wang, Kun, E-mail: wangkun@ujs.edu.cn [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013 (China)

    2016-12-15

    In this work, a novel homogeneous assay for DNA quantitative analysis based on förster resonance energy transfer (FRET) was developed for cauliflwer mosaic virus 35s (CaMV35S) promoter of transgenic soybean detection. The homogenous FRET of fluorescence signal was fabricated by DNA hybridization with probe modified nitrogen-doped graphene quantum dots (NGQDs) and silver nanoparticles (AgNPs), which acted the donor-acceptor pairs for the first time. The highly efficient FRET and unique properties of the NGQDs made the proposed FRET system as a functionalized detection platform for labelling of DNA. Upon the recognition of specific target DNA (tDNA), the FRET between NGQDs and AgNPs was triggered to produce fluorescence quenching, which could be used for tDNA detection. The fabricated homogeneous FRET assay displayed a wide linear range of 0.1–500.0 nM and a low limit of detection 0.03 nM for the detection of CaMV35S (S/N = 3). This proposed biosensor revealed high specificity to detect tDNA, with acceptable intra-assay precision and excellent stability. This method was successfully applied to identify the real sample of 0.5% containing transgenic soybean, which achieved the most of national law regulations. This assay was further validated by polymerase chain reaction as the genetically modified organisms, suggesting that the proposed FRET system is a feasible tool for the further daily genetically modified organism detection. - Highlights: • Both NGQDs and AgNPs were selected as the novel FRET donor-acceptor pairs. • The proposed homogeneous FRET assay was developed for CaMV35S detection. • The resulting method could identify 0.5% containing transgenic soybean sample. • This assay was inexpensive, simple and highly sensitive.

  10. Diagnosis of soft faults in analog integrated circuits based on fractional correlation

    International Nuclear Information System (INIS)

    Deng Yong; Shi Yibing; Zhang Wei

    2012-01-01

    Aiming at the problem of diagnosing soft faults in analog integrated circuits, an approach based on fractional correlation is proposed. First, the Volterra series of the circuit under test (CUT) decomposed by the fractional wavelet packet are used to calculate the fractional correlation functions. Then, the calculated fractional correlation functions are used to form the fault signatures of the CUT. By comparing the fault signatures, the different soft faulty conditions of the CUT are identified and the faults are located. Simulations of benchmark circuits illustrate the proposed method and validate its effectiveness in diagnosing soft faults in analog integrated circuits. (semiconductor integrated circuits)

  11. The Use of Two-Photon FRET-FLIM to Study Protein Interactions During Nuclear Envelope Fusion In Vivo and In Vitro.

    Science.gov (United States)

    Byrne, Richard D; Larijani, Banafshé; Poccia, Dominic L

    2016-01-01

    FRET-FLIM techniques have wide application in the study of protein and protein-lipid interactions in cells. We have pioneered an imaging platform for accurate detection of functional states of proteins and their interactions in fixed cells. This platform, two-site-amplified Förster resonance energy transfer (a-FRET), allows greater signal generation while retaining minimal noise thus enabling application of fluorescence lifetime imaging microscopy (FLIM) to be routinely deployed in different types of cells and tissue. We have used the method described here, time-resolved FRET monitored by two-photon FLIM, to demonstrate the direct interaction of Phospholipase Cγ (PLCγ) by Src Family Kinase 1 (SFK1) during nuclear envelope formation and during male and female pronuclear membrane fusion in fertilized sea urchin eggs. We describe here a generic method that can be applied to monitor any proteins of interest.

  12. Genome-wide identification and characterization of Notch transcription complex-binding sequence paired sites in leukemia cells

    Science.gov (United States)

    Severson, Eric; Arnett, Kelly L.; Wang, Hongfang; Zang, Chongzhi; Taing, Len; Liu, Hudan; Pear, Warren S.; Liu, X. Shirley; Blacklow, Stephen C.; Aster, Jon C.

    2018-01-01

    Notch transcription complexes (NTCs) drive target gene expression by binding to two distinct types of genomic response elements, NTC monomer-binding sites and sequence-paired sites (SPSs) that bind NTC dimers. SPSs are conserved and are linked to the Notch-responsiveness of a few genes, but their overall contribution to Notch-dependent gene regulation is unknown. To address this issue, we determined the DNA sequence requirements for NTC dimerization using a fluorescence resonance energy transfer (FRET) assay, and applied insights from these in vitro studies to Notch-“addicted” leukemia cells. We find that SPSs contribute to the regulation of approximately a third of direct Notch target genes. While originally described in promoters, SPSs are present mainly in long-range enhancers, including an enhancer containing a newly described SPS that regulates HES5. Our work provides a general method for identifying sequence-paired sites in genome-wide data sets and highlights the widespread role of NTC dimerization in Notch-transformed leukemia cells. PMID:28465412

  13. Base pair mismatches and carcinogen-modified bases in DNA: an NMR study of G x T and G x O4meT pairing in dodecanucleotide duplexes

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Kouchakdjian, M.; Li, B.F.L.; Swann, P.F.; Patel, D.J.

    1988-01-01

    High-resolution two-dimensional NMR studies have been completed on the self-complementary d(C-G-C-G-A-G-C-T-T-G-C-G) duplex (designated G x T 12-mer) and the self-complementary d(C-G-C-G-A-G-C-T-O 4 meT-G-C-G) duplex (designated G x O 4 meT 12-mer) containing G x T and G x O 4 meT pairs at identical positions four base pairs in from either end of the duplex. The exchangeable and nonexchangeable proton resonances have been assigned from an analysis of two-dimensional nuclear Overhauser enhancement (NOESY) spectra for the G x T 12-mer and G x O 4 meT 12-mer duplexes in H 2 O and D 2 O solution. The guanosine and thymidine imino protons in the G x T mismatch resonate at 10.57 and 11.98 ppm, respectively, and exhibit a strong NOE between themselves and to imino protons of flanking base pairs in the G x T 12-mer duplex. The large upfield chemical shift of this proton relative to that of the imino proton resonance of G in the G x T mismatch or in G x C base pairs indicates that hydrogen bonding to O 4 meT is either very weak or absent. This guanosine imino proton has an NOE to the OCH 3 group of O 4 meT across the pair and NOEs to the imino protons of flanking base pairs. Taken together with data from the NMR of nonexchangeable protons, this shows that both G and O 4 meT have anti-glycosidic torsion angles and are stacked into the duplex. Comparison of the intensity of the NOEs between the guanosine imino proton and the OCH 3 of O 4 meT as well as other protons in its vicinity demonstrates that the OCH 3 group of O 4 meT adopts the syn orientation with respect to N3 of the methylated thymidine. The authors propose an alternate base pairing mode stabilized by one short hydrogen bond between the 2-amino group of guanosine and the 2-carbonyl group of O 4 met

  14. All paired up with no place to go: pairing, synapsis, and DSB formation in a balancer heterozygote.

    Directory of Open Access Journals (Sweden)

    Wei J Gong

    2005-11-01

    Full Text Available The multiply inverted X chromosome balancer FM7 strongly suppresses, or eliminates, the occurrence of crossing over when heterozygous with a normal sequence homolog. We have utilized the LacI-GFP: lacO system to visualize the effects of FM7 on meiotic pairing, synapsis, and double-strand break formation in Drosophila oocytes. Surprisingly, the analysis of meiotic pairing and synapsis for three lacO reporter couplets in FM7/X heterozygotes revealed they are paired and synapsed during zygotene/pachytene in 70%-80% of oocytes. Moreover, the regions defined by these lacO couplets undergo double-strand break formation at normal frequency. Thus, even complex aberration heterozygotes usually allow high frequencies of meiotic pairing, synapsis, and double-strand break formation in Drosophila oocytes. However, the frequencies of failed pairing and synapsis were still 1.5- to 2-fold higher than were observed for corresponding regions in oocytes with two normal sequence X chromosomes, and this effect was greatest near a breakpoint. We propose that heterozygosity for breakpoints creates a local alteration in synaptonemal complex structure that is propagated across long regions of the bivalent in a fashion analogous to chiasma interference, which also acts to suppress crossing over.

  15. A Loudness Function for Analog and Digital Sound Systems based on Equal Loudness Level Contours

    DEFF Research Database (Denmark)

    Nielsen, Sofus Birkedal

    2016-01-01

    frequency balance will been changed both for LL lower or higher than ML. The differences in ELLC ask for a level based equalization using fractional-order filters. A designing technique for both analog and digital fractional-order filters was developed. The analog solution is based on OPAMs and the digital......A new and better loudness compensation has been designed based on the differences between the Equal Loudness Level Contours (ELLC) in ISO 226:2003. Sound productions are normally being mixed at a high mixing level (ML) but often played at lower listening level (LL) which mean that the perceived...

  16. Text Based Analogy in Overcoming Student Misconception on Simple Electricity Circuit Material

    Science.gov (United States)

    Hesti, R.; Maknun, J.; Feranie, S.

    2017-09-01

    Some researcher have found that the use of analogy in learning and teaching physics was effective enough in giving comprehension in a complicated physics concept such as electrical circuits. Meanwhile, misconception become main cause that makes students failed when learning physics. To provide teaching physics effectively, the misconception should be resolved. Using Text Based Analogy is one of the way to identifying misconceptions and it is enough to assist teachers in conveying scientific truths in order to overcome misconceptions. The purpose of the study to investigate the use of text based analogy in overcoming students misconception on simple electrical circuit material. The samples of this research were 28 of junior high school students taken purposively from one high school in South Jakarta. The method use in this research is pre-experimental and design in one shot case study. Students who are the participants of sample have been identified misconception on the electrical circuit material by using the Diagnostic Test of Simple Electricity Circuit. The results of this study found that TBA can replace the misconceptions of the concept possessed by students with scientific truths conveyed in the text in a way that is easily understood so that TBA is strongly recommended to use in other physics materials.

  17. Micromechanics of base pair unzipping in the DNA duplex

    International Nuclear Information System (INIS)

    Volkov, Sergey N; Paramonova, Ekaterina V; Yakubovich, Alexander V; Solov’yov, Andrey V

    2012-01-01

    All-atom molecular dynamics (MD) simulations of DNA duplex unzipping in a water environment were performed. The investigated DNA double helix consists of a Drew-Dickerson dodecamer sequence and a hairpin (AAG) attached to the end of the double-helix chain. The considered system is used to examine the process of DNA strand separation under the action of an external force. This process occurs in vivo and now is being intensively investigated in experiments with single molecules. The DNA dodecamer duplex is consequently unzipped pair by pair by means of the steered MD. The unzipping trajectories turn out to be similar for the duplex parts with G⋅C content and rather distinct for the parts with A⋅T content. It is shown that during the unzipping each pair experiences two types of motion: relatively quick rotation together with all the duplex and slower motion in the frame of the unzipping fork. In the course of opening, the complementary pair passes through several distinct states: (i) the closed state in the double helix, (ii) the metastable preopened state in the unzipping fork and (iii) the unbound state. The performed simulations show that water molecules participate in the stabilization of the metastable states of the preopened base pairs in the DNA unzipping fork. (paper)

  18. Fiber Fabry-Perot Force Sensor with Small Volume and High Performance for Assessing Fretting Damage of Steam Generator Tubes.

    Science.gov (United States)

    Huang, Peijian; Wang, Ning; Li, Junying; Zhu, Yong; Zhang, Jie

    2017-12-13

    Measuring the radial collision force between the steam generator tube (SGT) and the tube support plate (TSP) is essential to assess the fretting damage of the SGT. In order to measure the radial collision force, a novel miniaturized force sensor based on fiber Fabry-Perot (F-P) was designed, and the principle and characteristics of the sensor were analyzed in detail. Then, the F-P force sensor was successfully fabricated and calibrated, and the overall dimensions of the encapsulated fiber F-P sensor were 17 mm × 5 mm × 3 mm (L × W × H). The sensor works well in humid, high pressure (10 MPa), high temperature (350 °C), and vibration (40 kHz) environments. Finally, the F-P force sensors were installed in a 1:1 steam generator test loop, and the radial collision force signals between the SGT and the TSP were obtained. The experiments indicated that the F-P sensor with small volume and high performance could help in assessing the fretting damage of the steam generator tubes.

  19. Intramolecular ex vivo Fluorescence Resonance Energy Transfer (FRET of Dihydropyridine Receptor (DHPR β1a Subunit Reveals Conformational Change Induced by RYR1 in Mouse Skeletal Myotubes.

    Directory of Open Access Journals (Sweden)

    Dipankar Bhattacharya

    Full Text Available The dihydropyridine receptor (DHPR β1a subunit is essential for skeletal muscle excitation-contraction coupling, but the structural organization of β1a as part of the macromolecular DHPR-ryanodine receptor type I (RyR1 complex is still debatable. We used fluorescence resonance energy transfer (FRET to probe proximity relationships within the β1a subunit in cultured skeletal myotubes lacking or expressing RyR1. The fluorescein biarsenical reagent FlAsH was used as the FRET acceptor, which exhibits fluorescence upon binding to specific tetracysteine motifs, and enhanced cyan fluorescent protein (CFP was used as the FRET donor. Ten β1a reporter constructs were generated by inserting the CCPGCC FlAsH binding motif into five positions probing the five domains of β1a with either carboxyl or amino terminal fused CFP. FRET efficiency was largest when CCPGCC was positioned next to CFP, and significant intramolecular FRET was observed for all constructs suggesting that in situ the β1a subunit has a relatively compact conformation in which the carboxyl and amino termini are not extended. Comparison of the FRET efficiency in wild type to that in dyspedic (lacking RyR1 myotubes revealed that in only one construct (H458 CCPGCC β1a -CFP FRET efficiency was specifically altered by the presence of RyR1. The present study reveals that the C-terminal of the β1a subunit changes conformation in the presence of RyR1 consistent with an interaction between the C-terminal of β1a and RyR1 in resting myotubes.

  20. A language based on analogy to communicate cultural concepts in SETI

    Science.gov (United States)

    Musso, Paolo

    2011-02-01

    The present paper is a synthesis of three presentation given by myself at the Toulouse IAC 2001 ( Analogy as a tool to communicate abstract concepts in SETI), the Bremen IAC 2003 ( From maths to culture: towards an effective message), and the Vancouver IAC 2004 ( Philosophical and religious implications of extraterrestrial intelligent life). Its aim is to find a way to make our cultural concepts understandable to hypothetical extraterrestrials (ETs) in a SETI communication. First of all, I expose the reasons why I think that analogy could be a good tool for this purpose. Then, I try to show that this is possible only in the context of an integrated language, using both abstract symbols and pictures, also sketching two practical examples about some basic concepts of our moral and religious tradition. Further studies are required to determine whether this method could be extended to the higher-level abstract concepts in the other fields of our culture. Finally, I discuss the possible role of mathematics, logic and natural science in the construction of an analogy-based language for interstellar messages with a cultural content and a possible way of managing this matter from a social point of view.

  1. NOTE TAKING PAIRS TO IMPROVE STUDENTS‟ SENTENCE BASED WRITING ACHIEVEMENT

    Directory of Open Access Journals (Sweden)

    Testiana Deni Wijayatiningsih

    2017-04-01

    Full Text Available Students had skill to actualize their imagination and interpret their knowledge through writing which could be combined with good writing structure. Moreover, their writing skill still had low motivation and had not reached the standard writing structure. Based on the background above, this research has purpose to know the influence Note Taking Pairs in improving students‘sentence based writing achievement. The subject of this research was the second semester of English Department in Muhammadiyah University of Semarang. It also used statistic non parametric method to analyze the students‘ writing achievement. The result of this research showed that Note Taking Pairs strategy could improve students‘sentence based writing achievement. Hopefully this research is recommended into learning process to improve students‘writing skill especially in sentence-based writing subject.

  2. AT base pair anions versus (9-methyl-A)(1-methyl-T) base pair anions.

    Science.gov (United States)

    Radisic, Dunja; Bowen, Kit H; Dabkowska, Iwona; Storoniak, Piotr; Rak, Janusz; Gutowski, Maciej

    2005-05-04

    The anionic base pairs of adenine and thymine, (AT)(-), and 9-methyladenine and 1-methylthymine, (MAMT)(-), have been investigated both theoretically and experimentally in a complementary, synergistic study. Calculations on (AT)(-) found that it had undergone a barrier-free proton transfer (BFPT) similar to that seen in other dimer anion systems and that its structural configuration was neither Watson-Crick (WC) nor Hoogsteen (HS). The vertical detachment energy (VDE) of (AT)(-) was determined by anion photoelectron spectroscopy and found to be in agreement with the VDE value predicted by theory for the BFPT mechanism. An AT pair in DNA is structurally immobilized into the WC configuration, in part, by being bonded to the sugars of the double helix. This circumstance was mimicked by methylating the sites on both A and T where these sugars would have been tied, viz., 9-methyladenine and 1-methylthymine. Calculations found no BFPT in (MAMT)(-) and a resulting (MAMT)(-) configuration that was either HS or WC, with the configurations differing in stability by ca. 2 kcal/mol. The photoelectron spectrum of (MAMT)(-) occurred at a completely different electron binding energy than had (AT)(-). Moreover, the VDE value of (MAMT)(-) was in agreement with that predicted by theory. The configuration of (MAMT)(-) and its lack of electron-induced proton transfer are inter-related. While there may be other pathways for electron-induced DNA alterations, BFPT in the WC/HS configurations of (AT)(-) is not feasible.

  3. AT Base Pair Anions vs. (9-methyl-A)(1-methyl-T) Base Pair Anions

    International Nuclear Information System (INIS)

    Radisic, Dunja; Bowen, Kit H.; Dabkowska, Iwona; Storoniak, Piotr; Rak, Janusz; Gutowski, Maciej S.

    2005-01-01

    The anionic base pairs of adenine and thymine, (AT)-, and 9-methyladenine and 1-methylthymine, (MAMT)-, have been investigated both theoretically and experimentally in a complementary, synergistic study. Calculations on (AT)- found that it had undergone a barrier-free proton transfer (BFPT) similar to that seen in other dimer anion systems and that its structural configuration that was neither Watson-Crick (WC) nor Hoogsteen (HS). The vertical detachment energy (VDE) of (AT)- was determined by anion photoelectron spectroscopy and found to be in agreement with the VDE value predicted by theory for the BFPT mechanism. An AT pair in DNA is structurally immobilized into the WC configuration, in part, by being bonded to the sugars of the double helix. This circumstance was mimicked by methylating the sites on both A and T where these sugars would have been tied, viz., 9-methyladenine and 1-methylthymine. Calculations found no BFPT in (MAMT)- and a resulting (MAMT)- configuration that wa s either HS or WC, with the configurations differing in stability by ca. 2 kcal/mol. The photoelectron spectrum of (MAMT)- occurred at a completely different electron binding energy than had (AT)-. Moreover, the VDE value of (MAMT)- was in agreement with that predicted by theory. The configuration of (MAMT)- and its lack of electron-induced proton transfer are inter-related. While there may be other pathways for electron-induced damage, BFPT in the WC/HS configurations of (AT)- is not feasible

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

    KAUST Repository

    Chawla, Mohit

    2015-06-27

    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.

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

    KAUST Repository

    Chawla, Mohit; Oliva, R.; Bujnicki, J. 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.

  6. CsI Calorimeter for a Compton-Pair Telescope

    Science.gov (United States)

    Grove, Eric J.

    -reduction prototype telescope, Proto-ComPair. We will: 1. Purchase CsI(Tl) crystals, Silicon Photomultipliers (SiPMs), and components for the analog and digital readout of the SiPMs; 2. Assemble and test Crystal Detector Elements (CDEs) from crystals, SiPMs and optical wrap; 3. Assemble and test analog and digital front-end and readout control boards; 4. Fabricate the mechanical structure that supports and contains the CDEs and electronics boards; and 5. Assemble and test the CsI calorimeter, and integrate it with the remainder of the Proto-ComPair subsystems. The PI team for this proposal conceived, designed, developed, assembled, tested, and currently operates the LAT calorimeter and is uniquely qualified to leverage the experience gained from that effort for ComPair.

  7. Doubling-resolution analog-to-digital conversion based on PIC18F45K80

    Directory of Open Access Journals (Sweden)

    Yueyang Yuan

    2014-08-01

    Full Text Available Aiming at the analog signal being converted into the digital with a higher precision, a method to improve the analog-to-digital converter (ADC resolution is proposed and described. Based on the microcomputer PIC18F45K80 in which the internal ADC modules are embedded, a circuit is designed for doubling the resolution of ADC. According to the circuit diagram, the mathematical formula for calculating this resolution is derived. The corresponding software and print circuit board assembly is also prepared. With the experiment, a 13 bit ADC is achieved based on the 12 bit ADC module predesigned in the PIC18F45K80.

  8. Quantum walks based on an interferometric analogy

    International Nuclear Information System (INIS)

    Hillery, Mark; Bergou, Janos; Feldman, Edgar

    2003-01-01

    There are presently two models for quantum walks on graphs. The ''coined'' walk uses discrete-time steps, and contains, besides the particle making the walk, a second quantum system, the coin, that determines the direction in which the particle will move. The continuous walk operates with continuous time. Here a third model for quantum walks is proposed, which is based on an analogy to optical interferometers. It is a discrete-time model, and the unitary operator that advances the walk one step depends only on the local structure of the graph on which the walk is taking place. This type of walk also allows us to introduce elements, such as phase shifters, that have no counterpart in classical random walks. Several examples are discussed

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

    Science.gov (United States)

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

    2015-01-01

    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. 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. 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. 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%. 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.

  10. Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae

    OpenAIRE

    Lang, Gregory I.; Murray, Andrew W.

    2008-01-01

    Although mutation rates are a key determinant of the rate of evolution they are difficult to measure precisely and global mutations rates (mutations per genome per generation) are often extrapolated from the per-base-pair mutation rate assuming that mutation rate is uniform across the genome. Using budding yeast, we describe an improved method for the accurate calculation of mutation rates based on the fluctuation assay. Our analysis suggests that the per-base-pair mutation rates at two genes...

  11. Fretting wear of ZrN and Zr(21% Hf)N coatings

    Energy Technology Data Exchange (ETDEWEB)

    Atar, E. [Gebze Inst. of Tech., Material Science and Engineering Dept., Kocaeli (Turkey); Cimenoglu, H.; Kayali, E.S. [Istanbul Technical Univ., Dept. of Metallurgy and Materials Engineering, Istanbul (Turkey)

    2004-07-01

    In this study, the wear behaviours of ZrN and Zr(21% Hf)N coatings, deposited on hardened AISI D2 cold work tool steel were examined by a fretting wear tester. The hardness of ZrN and Zr(21% Hf)N coatings were almost the same, where as they exhibited different wear resistance. Addition of 21% Hf to ZrN coating achieved about 25% increase in the wear resistance. (orig.)

  12. Fretting wear of ZrN and Zr(21% Hf)N coatings

    International Nuclear Information System (INIS)

    Atar, E.; Cimenoglu, H.; Kayali, E.S.

    2004-01-01

    In this study, the wear behaviours of ZrN and Zr(21% Hf)N coatings, deposited on hardened AISI D2 cold work tool steel were examined by a fretting wear tester. The hardness of ZrN and Zr(21% Hf)N coatings were almost the same, where as they exhibited different wear resistance. Addition of 21% Hf to ZrN coating achieved about 25% increase in the wear resistance. (orig.)

  13. The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone

    DEFF Research Database (Denmark)

    Kumar, P.; Sharma, P. K.; Madsen, Charlotte S.

    2013-01-01

    Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand.......Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand....

  14. Nuclear squid: Diabolic pair transfer in rotating nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Nikam, R S; Ring, P; Canto, L F

    1987-02-19

    A new unexpected behavior of pair transfer matrix elements in superfluid rotating nuclei is predicted. With increasing angular velocity they drop to zero, change their sign and in some cases even oscillate between positive and negative values. This effect is related to diabolical points in rotating quasiparticle spectra and is closely analogous to the DC-Josephson effect in superconductors in the presence of a magnetic field.

  15. Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

    KAUST Repository

    Chawla, Mohit

    2013-10-10

    The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).

  16. Forster Resonance Energy Transfer (FRET) Analysis of Dual CFP/YFP Labeled AMPA Receptors Reveals Structural Rearrangement within the C-Terminal Domain during Receptor Activation

    DEFF Research Database (Denmark)

    Zachariassen, Linda Grønborg; Katchan, Mila; Plested, Andrew

    2014-01-01

    that retain function and display intrareceptor FRET. This includes a construct (GluA2-6Y-10C) containing YFP in the intracellular loop between the M1 and M2 membrane-embedded segments and CFP inserted in the C-ter- minal domain (CTD). GluA2-6Y-10C displays FRET with an efficiency of 0.11 while retaining wild......-type receptor expression and kinetic properties. We have used GluA2-6Y-10C to study conformational changes in homomeric GluA2 receptors during receptor activation. Our results show that the FRET efficiency is dependent on functional state of GluA2-6Y-10C and hereby indi- cates that the intracellular CTD...

  17. DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

    Science.gov (United States)

    Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

    2012-10-11

    Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

  18. The effects of similarity of theme and instantiation in analogical reasoning.

    Science.gov (United States)

    Yanowitz, K L

    2001-01-01

    The influence of 2 types of structural similarity on analogical reasoning was examined. The theme of a story is a structural component that constrains other relationships in the story. Another structural component is the way in which the theme is implemented. Participants received pairs of stories that varied in the similarity of these two components. Participants in Experiment 1 judged stories containing similar themes as more analogous than stories with dissimilar themes. Likewise, stories with similar implementations were judged as more analogous than stories with dissimilar implementations. Experiment 2 revealed a similar pattern when participants had the opportunity to transfer information from source to target stories. Greater transfer was seen for stories with similar themes than for stories with dissimilar themes. Greater transfer was also seen for stories with similar implementations of different themes than for stories with different implementations.

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

    Science.gov (United States)

    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

  20. Time-resolved UV-excited microarray reader for fluorescence energy transfer (FRET) measurements

    Science.gov (United States)

    Orellana, Adelina; Hokkanen, Ari P.; Pastinen, Tomi; Takkinen, Kristina; Soderlund, Hans

    2001-05-01

    Analytical systems based on immunochemistry are largely used in medical diagnostics and in biotechnology. There is a significant pressure to develop the present assay formats to become easier to use, faster, and less reagent consuming. Further developments towards high density array--like multianalyte measurement systems would be valuable. To this aim we have studied the applicability of fluorescence resonance energy transfer and time-resolved fluorescence resonance energy transfer in immunoassays on microspots and in microwells. We have used engineered recombinant antibodies detecting the pentameric protein CRP as a model analyte system, and tested different assay formats. We describe also the construction of a time-resolved scanning epifluorometer with which we could measure the FRET interaction between the slow fluorescence decay from europium chelates and its energy transfer to the rapidly decaying fluorophore Cy5.

  1. Stability of non-Watson-Crick G-A/A-G base pair in synthetic DNA and RNA oligonucleotides.

    Science.gov (United States)

    Ito, Yuko; Sone, Yumiko; Mizutani, Takaharu

    2004-03-01

    A non-Watson-Crick G-A/A-G base pair is found in SECIS (selenocysteine-insertion sequence) element in the 3'-untranslated region of Se-protein mRNAs and in the functional site of the hammerhead ribozyme. We studied the stability of G-A/A-G base pair (bold) in 17mer GT(U)GACGGAAACCGGAAC synthetic DNA and RNA oligonucleotides by thermal melting experiments and gel electrophoresis. The measured Tm value of DNA oligonucleotide having G-A/A-G pair showed an intermediate value (58 degrees C) between that of Watson-Crick G-C/C-G base pair (75 degrees C) and that of G-G/A-A of non-base-pair (40 degrees C). Similar thermal melting patterns were obtained with RNA oligonucleotides. This result indicates that the secondary structure of oligonucleotide having G-A/A-G base pair is looser than that of the G-C type Watson-Crick base pair. In the comparison between RNA and DNA having G-A/A-G base pair, the Tm value of the RNA oligonucleotide was 11 degrees C lower than that of DNA, indicating that DNA has a more rigid structure than RNA. The stained pattern of oligonucleotide on polyacrylamide gel clarified that the mobility of the DNA oligonucleotide G-A/A-G base pair changed according to the urea concentration from the rigid state (near the mobility of G-C/C-G oligonucleotide) in the absence of urea to the random state (near the mobility of G-G/A-A oligonucleotide) in 7 M urea. However, the RNA oligonucleotide with G-A/A-G pair moved at an intermediate mobility between that of oligonucleotide with G-C/C-G and of the oligonucleotide with G-G/A-A, and the mobility pattern did not depend on urea concentration. Thus, DNA and RNA oligonucleotides with the G-A/A-G base pair showed a pattern indicating an intermediate structure between the rigid Watson-Crick base pair and the random structure of non-base pair. RNA with G-A/A-G base pair has the intermediate structure not influenced by urea concentration. Finally, this study indicated that the intermediate rigidity imparted by Non

  2. Lewis pair polymerization by classical and frustrated Lewis pairs: Acid, base and monomer scope and polymerization mechanism

    KAUST Repository

    Zhang, Yuetao

    2012-01-01

    Classical and frustrated Lewis pairs (LPs) of the strong Lewis acid (LA) Al(C 6F 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 6F 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 6F 5) 3, can render highly active and effective LPP of MMA and γ-MMBL; such LBs include phosphines (e.g., P tBu 3), chiral chelating diphosphines, N-heterocyclic carbenes (NHCs), and phosphazene superbases (e.g., P 4- tBu). The P 4- tBu/Al(C 6F 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 γMMBL 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 6F 5) 3 adduct with P tBu 3 and NHC bases, respectively. Kinetic studies have revealed that the MMA polymerization by the tBu 3P/ Al(C 6F 5) 3 pair is zero-order in monomer concentration after an initial induction period, and the polymerization

  3. Performance Effects of Display Incogruity in a Digital and Analog Clock Reading Task

    Science.gov (United States)

    Comstock, J. Raymond, Jr.; Derks, Peter L.

    2004-01-01

    In an era of increasing automation, it is important to design displays and input devices that minimize human error. In this context, information concerning the human response to the detection of incongruous information is important. Such incongruous information can be operationalized as unexpected (perhaps erroneous) information on which a decision by the human or operation by an automated system is based. In the aviation environment, decision making when faced with inadequate, incomplete, or incongruous information may occur in a failure scenario. An additional challenge facing the human operator in automated environments is maintaining alertness or vigilance. The vigilance issue is of particular concern as a factor that may interact with performance when faced with inadequate, incomplete, or incongruous information. From the literature on eye-scan behavior we know that the time spent looking at a particular display or indicator is a function of the type of information one is trying to discern from the display. For example, quick glances are all it takes for confirming that an indicator is in a normal position or range, whereas a continuous look of several seconds may be required for confirmation that a complex control input is having the desired effect. Important to consider is that while an extended look takes place, visual input from other sources may be missed. Much like an extended look, the interpretation of incongruous information may require extra time. The present experiment was designed to explore the performance consequences of a decision making task when incongruous information was presented. For this experiment a display incongruity was created on a subset of trials of a clock reading laboratory task. Display incongruity was made possible through presentation of 'impossible' times (e.g. 1:65 or 11:90). Subjects made 'same' 'different' decisions and keyboard responses to pairings of Analog-Analog (AA), Digital-Digital (DD), and Analog- Digital (AD

  4. Predicting the Mechanism and Kinetics of the Watson-Crick to Hoogsteen Base Pairing Transition

    NARCIS (Netherlands)

    Vreede, J.; Bolhuis, P.G.; Swenson, D.W.H.

    2016-01-01

    DNA duplexes predominantly contain Watson-Crick (WC) base pairs. Yet, a non-negligible number of base pairs converts to the Hoogsteen (HG) hydrogen bonding pattern, involving a 180° rotation of the purine base relative to Watson-Crick. These WC to HG conversions alter the conformation of DNA, and

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2014-01-08

    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.

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

    Science.gov (United States)

    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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

    Graphical abstract: Reactions of methyldiazonium ion at the different sites of the DNA bases in the Watson-Crick GC and AT base pairs were investigated employing density functional and second order Moller-Plesset (MP2) perturbation theories. Display Omitted Highlights: → Methylation of the DNA bases is important as it can cause mutation and cancer. → Methylation reactions of the GC and AT base pairs with CH 3 N 2 + were not studied earlier theoretically. → Experimental observations have been explained using theoretical methods. - Abstract: 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 Moller-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.

  9. Existence and consequences of Coulomb pairing of electrons in a solid

    International Nuclear Information System (INIS)

    Mahajan, S.M.; Thyagaraja, A.

    1996-11-01

    It is shown from first principles that, in the periodic potential of a crystalline solid, short-range (i.e., screened) binary Coulomb interactions can lead to a two-electron bound state. It is further suggested that these composite bosonic states (charge -2e, and typically spin zero) could mediate an effectively attractive interaction between pairs of conduction electrons close to the Fermi level. This necessarily short range attractive interaction, which is crucially dependent on the band structure of the solid, and is complementary to the phonon-mediated one, may provide a source for the existence and properties of short correlation-length electron pairs (analogous to but distinct from Cooper pairs) needed to understand high temperature superconductivity. Several distinctive and observable characteristics of the proposed pairing scheme are discussed

  10. Charge transfer in DNA: role of base pairing

    Czech Academy of Sciences Publication Activity Database

    Kratochvílová, Irena; Bunček, M.; Schneider, Bohdan

    2009-01-01

    Roč. 38, Suppl. (2009), S123-S123 ISSN 0175-7571. [EBSA European Biophysics Congress /7./. Genoa, 11.07.2009-15.07.2009] Institutional research plan: CEZ:AV0Z10100520; CEZ:AV0Z50520701 Keywords : DNA * charge transport * base pairing Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.437, year: 2009

  11. A novel modulation scheme for noise reduction in analog fiber optic links

    NARCIS (Netherlands)

    Marpaung, D.A.I.; Roeloffzen, C.G.H.; van Etten, Wim; Megret, P.; Wuilpart, M.; Bette, S.; Staquet, N.

    2005-01-01

    A novel balanced modulation and detection scheme for analog fiber optic links is proposed to overcome the limitations in signal-to-noise ratio (SNR) and dynamic range (DR).In this scheme, the modulating signal is split into positive and negative halves and applied to a pair of laser diodes. Both

  12. arXiv On Matrix Factorizations, Residue Pairings and Homological Mirror Symmetry

    CERN Document Server

    Lerche, Wolfgang

    We argue how boundary B-type Landau-Ginzburg models based on matrix factorizations can be used to compute exact superpotentials for intersecting D-brane configurations on compact Calabi-Yau spaces. In this paper, we consider the dependence of open-string, boundary changing correlators on bulk moduli. This determines, via mirror symmetry, non-trivial disk instanton corrections in the A-model. As crucial ingredient we propose a differential equation that involves matrix analogs of Saito's higher residue pairings. As example, we compute from this for the elliptic curve certain quantum products m_2 and m_3, which reproduce genuine boundary changing, open Gromov-Witten invariants.

  13. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

    Science.gov (United States)

    Dixit, Surjit B; Mezei, Mihaly; Beveridge, David L

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the

  14. Photochemical selectivity in guanine-cytosine base-pair structures

    Czech Academy of Sciences Publication Activity Database

    Abo-Riziq, A.; Grace, L.; Nir, E.; Kabeláč, Martin; Hobza, Pavel; Vries de, M. S.

    2005-01-01

    Roč. 102, č. 1 (2005), s. 20-23 ISSN 0027-8424 R&D Projects: GA ČR(CZ) GA203/05/0009 Grant - others:NSF(US) CHE-0244341 Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA base pairs * IR-UV spectroscopy * phytochemistry Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 10.231, year: 2005

  15. Unlubricated Gross Slip Fretting Wear of Metallic Plasma Sprayed Coatings for Ti6A14V Surfaces

    National Research Council Canada - National Science Library

    Hager, Jr., Carl H; Sanders, Jeffrey H; Sharma, Shashi K

    2006-01-01

    ... to simulate cold engine startup. Alternative coatings such as plasma sprayed molybdenum and nickel were also evaluated because of their potential for reducing fretting wear under certain simulated engine conditions...

  16. Measurement and theory of hydrogen bonding contribution to isosteric DNA base pairs.

    Science.gov (United States)

    Khakshoor, Omid; Wheeler, Steven E; Houk, K N; Kool, Eric T

    2012-02-15

    We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions between F and natural bases in nucleic acid duplexes and in a DNA polymerase active site. Since F is widely used to measure electrostatic contributions to pairing and replication, it is important to quantify the impact of this isostere on DNA stability. Here, we studied the pairing stability and selectivity of this compound and a closely related variant, dichlorotoluene deoxyriboside (L), in DNA, using both experimental and computational approaches. We measured the thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners by thermal melting studies using the van't Hoff approach, and for selected cases by isothermal titration calorimetry (ITC). Experimental results showed that internal F-A pairing in DNA is destabilizing by 3.8 kcal/mol (van't Hoff, 37 °C) as compared with T-A pairing. At the end of a duplex, base-base interactions are considerably smaller; however, the net F-A interaction remains repulsive while T-A pairing is attractive. As for selectivity, F is found to be slightly selective for adenine over C, G, T by 0.5 kcal mol, as compared with thymine's selectivity of 2.4 kcal/mol. Interestingly, dichlorotoluene in DNA is slightly less destabilizing and slightly more selective than F, despite the lack of strongly electronegative fluorine atoms. Experimental data were complemented by computational results, evaluated at the M06-2X/6-31+G(d) and MP2/cc-pVTZ levels of theory. These computations suggest that the pairing energy of F to A

  17. Relation Education Index Norms for 500 Picture Pairs and 10 Relations: High School Sample. Technical Report No. 6.

    Science.gov (United States)

    Haynes, James L.; And Others

    Mode of presentation (word vs. picture) is said to be a factor in social class differences in performance on analogy tests. To investigate this contention, data were needed on equivalent word and picture analogy test performance. This report presents data on relation education index (REI) norms for 500 picture pairs collected in the process of…

  18. Application of Powell's analogy for the prediction of vortex-pairing sound in a low-Mach number jet based on time-resolved planar and tomographic PIV

    NARCIS (Netherlands)

    Violato, D.; Bryon, K.; Moore, P.; Scarano, F.

    2010-01-01

    This paper describes an experimental investigation by time-resolved planar and tomographic PIV on the sound production mechanism of vortex pairing of a transitional water-jet flow at Re=5000. The shear layer is characterized by axisymmetric vortex rings which undergo pairing with a varicose mode.

  19. Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics.

    Science.gov (United States)

    List, Johann-Mattis; Pathmanathan, Jananan Sylvestre; Lopez, Philippe; Bapteste, Eric

    2016-08-20

    For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields. We compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir's drift). Apart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to

  20. Finding faults: analogical comparison supports spatial concept learning in geoscience.

    Science.gov (United States)

    Jee, Benjamin D; Uttal, David H; Gentner, Dedre; Manduca, Cathy; Shipley, Thomas F; Sageman, Bradley

    2013-05-01

    A central issue in education is how to support the spatial thinking involved in learning science, technology, engineering, and mathematics (STEM). We investigated whether and how the cognitive process of analogical comparison supports learning of a basic spatial concept in geoscience, fault. Because of the high variability in the appearance of faults, it may be difficult for students to learn the category-relevant spatial structure. There is abundant evidence that comparing analogous examples can help students gain insight into important category-defining features (Gentner in Cogn Sci 34(5):752-775, 2010). Further, comparing high-similarity pairs can be especially effective at revealing key differences (Sagi et al. 2012). Across three experiments, we tested whether comparison of visually similar contrasting examples would help students learn the fault concept. Our main findings were that participants performed better at identifying faults when they (1) compared contrasting (fault/no fault) cases versus viewing each case separately (Experiment 1), (2) compared similar as opposed to dissimilar contrasting cases early in learning (Experiment 2), and (3) viewed a contrasting pair of schematic block diagrams as opposed to a single block diagram of a fault as part of an instructional text (Experiment 3). These results suggest that comparison of visually similar contrasting cases helped distinguish category-relevant from category-irrelevant features for participants. When such comparisons occurred early in learning, participants were more likely to form an accurate conceptual representation. Thus, analogical comparison of images may provide one powerful way to enhance spatial learning in geoscience and other STEM disciplines.

  1. Fretting and wear behaviors of Ni/nano-WC composite coatings in dry and wet conditions

    International Nuclear Information System (INIS)

    Benea, Lidia; Başa, Sorin-Bogdan; Dănăilă, Eliza; Caron, Nadège; Raquet, Olivier; Ponthiaux, Pierre; Celis, Jean-Pierre

    2015-01-01

    Highlights: • The friction and wear properties of Ni/nano-WC composite were studied. • Nano-WC reinforcement decreased friction coefficient in dry and wet conditions. • Nano-WC reinforcement fraction was seen to be 12 wt.%. • Nanohardness increased by 27% compared to nickel without WC reinforcements. • Ennoblement of OCP corresponding to the Ni/nano-WC composite coating. - Abstract: The fretting and wear behaviors of Ni/nano-WC composite coatings were studied by considering the effect of fretting frequency of 1 Hz during 10,000 cycles, at different applied loads in dry or wet conditions. The studies were performed on a ball-on-disk tribometer and the results were compared with pure Ni coating. The nanohardness of pure Ni and Ni/nano-WC composite coatings was tested by nanoindentation technique. To evaluate the wet wear (tribocorrosion) behavior the open circuit potential (OCP) was measured before, during and after the fretting tests at room temperature in the solution that simulates the primary water circuit of Pressurized Water Reactors (PWRs). The results show that Ni/nano-WC composite coatings exhibited a low friction coefficient, high nanohardness and wear resistance compared with pure Ni coatings under similar experimental conditions. Ni/nano-WC composite coatings were obtained on stainless steel support by electrochemical codeposition of nano-sized WC particles (diameter size of ∼60 nm) with nickel, from a standard nickel Watts plating bath. The surface morphology and the composition of the coatings were characterized by scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDX) respectively

  2. Principles of RNA base pairing: Structures and energies of cis and trans-Watson-Crick/Sugar Edge base pairs revealed by quantum chemical calculations

    Czech Academy of Sciences Publication Activity Database

    Šponer, Judit E.; Leszczynski, J.; Šponer, Jiří

    2005-01-01

    Roč. 22, č. 6 (2005), s. 826 ISSN 0739-1102. [Albany 2005. Conversation /14./. 14.06.2005-18.06.2005, Albany] Institutional research plan: CEZ:AV0Z50040507 Keywords : RNA base pairing * DNA * Watson-Crick/Sugar Edge Subject RIV: BO - Biophysics

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

    Science.gov (United States)

    Kondo, Jiro; Westhof, Eric

    2011-10-01

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

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

    Science.gov (United States)

    Kondo, Jiro; Westhof, Eric

    2011-01-01

    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

  5. Structural changes in the cytoplasmic pore of the Kir1.1 channel during pHi-gating probed by FRET.

    Science.gov (United States)

    Lee, Jay-Ron; Shieh, Ru-Chi

    2009-03-06

    Kir1.1 channels are important in maintaining K+ homeostasis in the kidney. Intracellular acidification reversibly closes the Kir1.1 channel and thus decreases K+ secretion. In this study, we used Foster resonance energy transfer (FRET) to determine whether the conformation of the cytoplasmic pore changes in response to intracellular pH (pHi)-gating in Kir1.1 channels fused with enhanced cyan fluorescent protein (ECFP) and enhanced yellow fluorescent protein (EYFP) (ECFP-Kir1.1-EYFP). Because the fluorescence intensities of ECFP and EYFP were affected at pHi pHi-gating occurs in the ECFP-Kir1.1-EYFP construct, we examined the FRET efficiencies of an ECFP-S219R-EYFP mutant, which is completed closed at pHi 7.4 and open at pHi 10.0. FRET efficiency was increased from 25% to 40% when the pHi was decreased from 10.0 to 7.4. These results suggest that the conformation of the cytoplasmic pore in the Kir1.1 channel changes in response to pHi gating such that the N- and C-termini move apart from each other at pHi 7.4, when the channel is open.

  6. Analogical scaffolding: Making meaning in physics through representation and analogy

    Science.gov (United States)

    Podolefsky, Noah Solomon

    This work reviews the literature on analogy, introduces a new model of analogy, and presents a series of experiments that test and confirm the utility of this model to describe and predict student learning in physics with analogy. Pilot studies demonstrate that representations (e.g., diagrams) can play a key role in students' use of analogy. A new model of analogy, Analogical Scaffolding, is developed to explain these initial empirical results. This model will be described in detail, and then applied to describe and predict the outcomes of further experiments. Two large-scale (N>100) studies will demonstrate that: (1) students taught with analogies, according to the Analogical Scaffolding model, outperform students taught without analogies on pre-post assessments focused on electromagnetic waves; (2) the representational forms used to teach with analogy can play a significant role in student learning, with students in one treatment group outperforming students in other treatment groups by factors of two or three. It will be demonstrated that Analogical Scaffolding can be used to predict these results, as well as finer-grained results such as the types of distracters students choose in different treatment groups, and to describe and analyze student reasoning in interviews. Abstraction in physics is reconsidered using Analogical Scaffolding. An operational definition of abstraction is developed within the Analogical Scaffolding framework and employed to explain (a) why physicists consider some ideas more abstract than others in physics, and (b) how students conceptions of these ideas can be modeled. This new approach to abstraction suggests novel approaches to curriculum design in physics using Analogical Scaffolding.

  7. 23rd workshop on Advances in Analog Circuit Design

    CERN Document Server

    Baschirotto, Andrea; Makinwa, Kofi

    2015-01-01

    This book is based on the 18 tutorials presented during the 23rd workshop on Advances in Analog Circuit Design.  Expert designers present readers with information about a variety of topics at the frontier of analog circuit design, serving as a valuable reference to the state-of-the-art, for anyone involved in analog circuit research and development.    • Includes coverage of high-performance analog-to-digital and digital to analog converters, integrated circuit design in scaled technologies, and time-domain signal processing; • Provides a state-of-the-art reference in analog circuit design, written by experts from industry and academia; • Presents material in a tutorial-based format.

  8. Computational approaches to analogical reasoning current trends

    CERN Document Server

    Richard, Gilles

    2014-01-01

    Analogical reasoning is known as a powerful mode for drawing plausible conclusions and solving problems. It has been the topic of a huge number of works by philosophers, anthropologists, linguists, psychologists, and computer scientists. As such, it has been early studied in artificial intelligence, with a particular renewal of interest in the last decade. The present volume provides a structured view of current research trends on computational approaches to analogical reasoning. It starts with an overview of the field, with an extensive bibliography. The 14 collected contributions cover a large scope of issues. First, the use of analogical proportions and analogies is explained and discussed in various natural language processing problems, as well as in automated deduction. Then, different formal frameworks for handling analogies are presented, dealing with case-based reasoning, heuristic-driven theory projection, commonsense reasoning about incomplete rule bases, logical proportions induced by similarity an...

  9. Chemical synthesis of dual labeled proteins via differently protected alkynes enables intramolecular FRET analysis.

    Science.gov (United States)

    Hayashi, Gosuke; Kamo, Naoki; Okamoto, Akimitsu

    2017-05-30

    We report a novel method for multisite protein conjugation by setting differently silyl-protected alkynes as conjugation handles, which can remain intact through the whole synthetic procedure and provide sequential and orthogonal conjugation. This strategy enables efficient preparation of a dual dye-labeled protein and structural analysis via an intramolecular FRET mechanism.

  10. Discrimination among individual Watson–Crick base pairs at the termini of single DNA hairpin molecules

    Science.gov (United States)

    Vercoutere, Wenonah A.; Winters-Hilt, Stephen; DeGuzman, Veronica S.; Deamer, David; Ridino, Sam E.; Rodgers, Joseph T.; Olsen, Hugh E.; Marziali, Andre; Akeson, Mark

    2003-01-01

    Nanoscale α-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson–Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5′ versus 3′ orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson–Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore. PMID:12582251

  11. Fast multichannel analog storage system

    International Nuclear Information System (INIS)

    Freytag, D.R.

    1982-11-01

    A Multichannel Analog Storage System based on a commercial 32-channel parallel in/serial out (PISO) analog shift register is described. The basic unit is a single width CAMAC module containing 512 analog cells and the associated logic for data storage and subsequent readout. At sampling rates of up to 30 MHz the signals are strobed directly into the PISO. At higher rates signals are strobed into a fast presampling stage and subsequently transferred in block form into an array of PISO's. Sampling rates of 300 MHz have been achieved with the present device and 1000 MHz are possible with improved signal drivers. The system is well suited for simultaneous handling of many signal channels with moderate numbers of samples in each channel. RMS noise over full scale signal has been measured as 1:3000 (approx. = 11 bit). However, nonlinearities in the response and differences in sensitivity of the analog cells require an elaborate calibration system in order to realize 11 bit accuracy for the analog information

  12. Solvent effects on hydrogen bonds in Watson-Crick, mismatched, and modified DNA base pairs

    NARCIS (Netherlands)

    Poater, Jordi; Swart, Marcel; Guerra, Celia Fonseca; Bickelhaupt, F. Matthias

    2012-01-01

    We have theoretically analyzed a complete series of Watson–Crick and mismatched DNA base pairs, both in gas phase and in solution. Solvation causes a weakening and lengthening of the hydrogen bonds between the DNA bases because of the stabilization of the lone pairs involved in these bonds. We have

  13. Mixing problem based learning and conventional teaching methods in an analog electronics course

    NARCIS (Netherlands)

    Podges, J M; Kommers, P A M; Winnips, K; van Joolingen, W R

    2014-01-01

    This study, undertaken at the Walter Sisulu University of Technology (WSU) in South Africa, describes how problem-based learning (PBL) affects the first year 'analog electronics course', when PBL and the lecturing mode is compared. Problems were designed to match real-life situations. Data between

  14. The use of Fluorescence Resonance Energy Transfer (FRET peptidesfor measurement of clinically important proteolytic enzymes

    Directory of Open Access Journals (Sweden)

    Adriana K. Carmona

    2009-09-01

    Full Text Available Proteolytic enzymes have a fundamental role in many biological processes and are associated with multiple pathological conditions. Therefore, targeting these enzymes may be important for a better understanding of their function and development of therapeutic inhibitors. Fluorescence Resonance Energy Transfer (FRET peptides are convenient tools for the study of peptidases specificity as they allow monitoring of the reaction on a continuous basis, providing a rapid method for the determination of enzymatic activity. Hydrolysis of a peptide bond between the donor/acceptor pair generates fluorescence that permits the measurement of the activity of nanomolar concentrations of the enzyme. The assays can be performed directly in a cuvette of the fluorimeter or adapted for determinations in a 96-well fluorescence plate reader. The synthesis of FRET peptides containing ortho-aminobenzoic acid (Abz as fluorescent group and 2, 4-dinitrophenyl (Dnp or N-(2, 4-dinitrophenylethylenediamine (EDDnp as quencher was optimized by our group and became an important line of research at the Department of Biophysics of the Federal University of São Paulo. Recently, Abz/Dnp FRET peptide libraries were developed allowing high-throughput screening of peptidases substrate specificity. This review presents the consolidation of our research activities undertaken between 1993 and 2008 on the synthesis of peptides and study of peptidases specificities.As enzimas proteolíticas têm um papel fundamental em muitos processos biológicos e estão associadas a vários estados patológicos. Por isso, o estudo da especificidade das peptidases pode ser importante para uma melhor compreensão da função destas enzimas e para o desenvolvimento de inibidores. Os substratos com supressão intramolecular de fluorescência constituem uma excelente ferramenta, pois permitem o monitoramento da reação de forma contínua, proporcionando um método prático e rápido para a determinação da

  15. Probing plasma membrane microdomains in cowpea protoplasts using lipidated GFP-fusion proteins and multimode FRET microscopy

    NARCIS (Netherlands)

    Vermeer, J.E.M.; van Munster, E.B.; Vischer, N.O.; Gadella, T.

    2004-01-01

    Multimode fluorescence resonance energy transfer (FRET) microscopy was applied to study the plasma membrane organization using different lipidated green fluorescent protein (GFP)-fusion proteins co-expressed in cowpea protoplasts. Cyan fluorescent protein (CFP) was fused to the hyper variable region

  16. Imaging molecular interactions in cells by dynamic and static fluorescence anisotropy (rFLIM and emFRET)

    NARCIS (Netherlands)

    Lidke, D.S.; Nagy, P.; Barisas, B.G.; Heintzmann, R.; Post, Janine Nicole; Lidke, K.A.; Clayton, A.H.A.; Arndt-jovin, D.J.; Jovin, T.M.

    2003-01-01

    We report the implementation and exploitation of fluorescence polarization measurements, in the form of anisotropy fluorescence lifetime imaging microscopy (rFLIM) and energy migration Förster resonance energy transfer (emFRET) modalities, for wide-field, confocal laser-scanning microscopy and flow

  17. KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

    Science.gov (United States)

    Betz, Karin; Malyshev, Denis A; Lavergne, Thomas; Welte, Wolfram; Diederichs, Kay; Dwyer, Tammy J; Ordoukhanian, Phillip; Romesberg, Floyd E; Marx, Andreas

    2012-07-01

    Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

  18. Evaluation of a FRET-peptide substrate to predict virulence in Pseudomonas aeruginosa.

    Directory of Open Access Journals (Sweden)

    Wendy E Kaman

    Full Text Available Pseudomonas aeruginosa produces a number of proteases that are associated with virulence and disease progression. A substrate able to detect P. aeruginosa-specific proteolytic activity could help to rapidly alert clinicians to the virulence potential of individual P. aeruginosa strains. For this purpose we designed a set of P. aeruginosa-specific fluorogenic substrates, comprising fluorescence resonance energy transfer (FRET-labeled peptides, and evaluated their applicability to P. aeruginosa virulence in a range of clinical isolates. A FRET-peptide comprising three glycines (3xGly was found to be specific for the detection of P. aeruginosa proteases. Further screening of 97 P. aeruginosa clinical isolates showed a wide variation in 3xGly cleavage activity. The absence of 3xGly degradation by a lasI knock out strain indicated that 3xGly cleavage by P. aeruginosa could be quorum sensing (QS-related, a hypothesis strengthened by the observation of a strong correlation between 3xGly cleavage, LasA staphylolytic activity and pyocyanin production. Additionally, isolates able to cleave 3xGly were more susceptible to the QS inhibiting antibiotic azithromycin (AZM. In conclusion, we designed and evaluated a 3xGly substrate possibly useful as a simple tool to predict virulence and AZM susceptibility.

  19. Ferrocene-based Lewis acids and Lewis pairs: Synthesis and ...

    Indian Academy of Sciences (India)

    The design and synthesis of molecules containing non-interacting Lewis base and Lewis acid groups. [Frustrated Lewis pairs (FLP's)] have received intense attention due to their potential applications in the area of molecular catalysis.1–3. For example,. Stephen's and co-workers have demonstrated that the unquenched ...

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

    Science.gov (United States)

    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.

  1. Analogical proportions: another logical view

    Science.gov (United States)

    Prade, Henri; Richard, Gilles

    This paper investigates the logical formalization of a restricted form of analogical reasoning based on analogical proportions, i.e. statements of the form a is to b as c is to d. Starting from a naive set theoretic interpretation, we highlight the existence of two noticeable companion proportions: one states that a is to b the converse of what c is to d (reverse analogy), while the other called paralogical proportion expresses that what a and b have in common, c and d have it also. We identify the characteristic postulates of the three types of proportions and examine their consequences from an abstract viewpoint. We further study the properties of the set theoretic interpretation and of the Boolean logic interpretation, and we provide another light on the understanding of the role of permutations in the modeling of the three types of proportions. Finally, we address the use of these proportions as a basis for inference in a propositional setting, and relate it to more general schemes of analogical reasoning. The differences between analogy, reverse-analogy, and paralogy is still emphasized in a three-valued setting, which is also briefly presented.

  2. Assessment of Corrosion, Fretting, and Material Loss of Retrieved Modular Total Knee Arthroplasties.

    Science.gov (United States)

    Martin, Audrey J; Seagers, Kirsten A; Van Citters, Douglas W

    2017-07-01

    Modular junctions in total hip arthroplasties have been associated with fretting, corrosion, and debris release. The purpose of this study is to analyze damage severity in total knee arthroplasties of a single design by qualitative visual assessment and quantitative material loss measurements to evaluate implant performance and patient impact via material loss. Twenty-two modular knee retrievals of the same manufacturer were identified from an institutional review board-approved database. Junction designs included tapers with an axial screw and tapers with a radial screw. Constructs consisted of 2 metal alloys: CoCr and Ti6Al4V. Components were qualitatively scored and quantitatively measured for corrosion and fretting. Negative values represent adhered material. Statistical differences were analyzed using sign tests. Correlations were tested with a Spearman rank order test (P corrosion than other components, suggesting preferential corrosion when interfacing with Ti6Al4V. Overall, although corrosion was noted in this series, material loss was low, and none were revised for clinical metal-related reaction. This suggests the clinical impact from corrosion in total knee arthroplasty is low. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Noninvasive High-Throughput Single-Cell Analysis of HIV Protease Activity Using Ratiometric Flow Cytometry

    Directory of Open Access Journals (Sweden)

    Rok Gaber

    2013-11-01

    Full Text Available To effectively fight against the human immunodeficiency virus infection/ acquired immunodeficiency syndrome (HIV/AIDS epidemic, ongoing development of novel HIV protease inhibitors is required. Inexpensive high-throughput screening assays are needed to quickly scan large sets of chemicals for potential inhibitors. We have developed a Förster resonance energy transfer (FRET-based, HIV protease-sensitive sensor using a combination of a fluorescent protein pair, namely mCerulean and mCitrine. Through extensive in vitro characterization, we show that the FRET-HIV sensor can be used in HIV protease screening assays. Furthermore, we have used the FRET-HIV sensor for intracellular quantitative detection of HIV protease activity in living cells, which more closely resembles an actual viral infection than an in vitro assay. We have developed a high-throughput method that employs a ratiometric flow cytometry for analyzing large populations of cells that express the FRET-HIV sensor. The method enables FRET measurement of single cells with high sensitivity and speed and should be used when subpopulation-specific intracellular activity of HIV protease needs to be estimated. In addition, we have used a confocal microscopy sensitized emission FRET technique to evaluate the usefulness of the FRET-HIV sensor for spatiotemporal detection of intracellular HIV protease activity.

  4. Noninvasive High-Throughput Single-Cell Analysis of HIV Protease Activity Using Ratiometric Flow Cytometry

    Science.gov (United States)

    Gaber, Rok; Majerle, Andreja; Jerala, Roman; Benčina, Mojca

    2013-01-01

    To effectively fight against the human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS) epidemic, ongoing development of novel HIV protease inhibitors is required. Inexpensive high-throughput screening assays are needed to quickly scan large sets of chemicals for potential inhibitors. We have developed a Förster resonance energy transfer (FRET)-based, HIV protease-sensitive sensor using a combination of a fluorescent protein pair, namely mCerulean and mCitrine. Through extensive in vitro characterization, we show that the FRET-HIV sensor can be used in HIV protease screening assays. Furthermore, we have used the FRET-HIV sensor for intracellular quantitative detection of HIV protease activity in living cells, which more closely resembles an actual viral infection than an in vitro assay. We have developed a high-throughput method that employs a ratiometric flow cytometry for analyzing large populations of cells that express the FRET-HIV sensor. The method enables FRET measurement of single cells with high sensitivity and speed and should be used when subpopulation-specific intracellular activity of HIV protease needs to be estimated. In addition, we have used a confocal microscopy sensitized emission FRET technique to evaluate the usefulness of the FRET-HIV sensor for spatiotemporal detection of intracellular HIV protease activity. PMID:24287545

  5. Priming analogical reasoning with false memories.

    Science.gov (United States)

    Howe, Mark L; Garner, Sarah R; Threadgold, Emma; Ball, Linden J

    2015-08-01

    Like true memories, false memories are capable of priming answers to insight-based problems. Recent research has attempted to extend this paradigm to more advanced problem-solving tasks, including those involving verbal analogical reasoning. However, these experiments are constrained inasmuch as problem solutions could be generated via spreading activation mechanisms (much like false memories themselves) rather than using complex reasoning processes. In three experiments we examined false memory priming of complex analogical reasoning tasks in the absence of simple semantic associations. In Experiment 1, we demonstrated the robustness of false memory priming in analogical reasoning when backward associative strength among the problem terms was eliminated. In Experiments 2a and 2b, we extended these findings by demonstrating priming on newly created homonym analogies that can only be solved by inhibiting semantic associations within the analogy. Overall, the findings of the present experiments provide evidence that the efficacy of false memory priming extends to complex analogical reasoning problems.

  6. Mixing Problem Based Learning And Conventional Teaching Methods In An Analog Electronics Course

    NARCIS (Netherlands)

    Podges, J.M.; Kommers, Petrus A.M.; Winnips, K.; van Joolingen, Wouter

    2014-01-01

    This study, undertaken at the Walter Sisulu University of Technology (WSU) in South Africa, describes how problem-based learning (PBL) affects the first year ‘analog electronics course’, when PBL and the lecturing mode is compared. Problems were designed to match real-life situations. Data between

  7. Event-Based Computation of Motion Flow on a Neuromorphic Analog Neural Platform

    Directory of Open Access Journals (Sweden)

    Massimiliano eGiulioni

    2016-02-01

    Full Text Available We demonstrate robust optical flow extraction with an analog neuromorphic multi-chip system. The task is performed by a feed-forward network of analog integrate-and-fire neurons whose inputs are provided by contrast-sensitive photoreceptors. Computation is supported by the precise time of spike emission and follows the basic theoretical principles presented in (Benosman et al. 2014: the extraction of the optical flow is based on time lag in the activation of nearby retinal neurons. The same basic principle is embedded in the architecture proposed by Barlow and Levick in 1965 to explain the spiking activity of the direction-selective ganglion cells in the rabbit's retina. Mimicking those cells our neuromorphic detectors encode the amplitude and the direction of the apparent visual motion in their output spiking pattern. We built a 3x3 test grid of independent detectors, each observing a different portion of the scene, so that our final output is a spike train encoding a 3x3 optical flow vector field. In this work we focus on the architectural aspects, and we demonstrate that a network of mismatched delicate analog elements can reliably extract the optical flow from a simple visual scene.

  8. Optimizing FRET-FLIM Labeling Conditions to Detect Nuclear Protein Interactions at Native Expression Levels in Living Arabidopsis Roots

    KAUST Repository

    Long, Yuchen; Stahl, Yvonne; Weidtkamp-Peters, Stefanie; Smet, Wouter; Du, Yujuan; Gadella, Theodorus W. J.; Goedhart, Joachim; Scheres, Ben; Blilou, Ikram

    2018-01-01

    Protein complex formation has been extensively studied using Förster resonance energy transfer (FRET) measured by Fluorescence Lifetime Imaging Microscopy (FLIM). However, implementing this technology to detect protein interactions in living

  9. Förster resonance energy transfer: Role of diffusion of fluorophore orientation and separation in observed shifts of FRET efficiency.

    Directory of Open Access Journals (Sweden)

    Bram Wallace

    Full Text Available Förster resonance energy transfer (FRET is a widely used single-molecule technique for measuring nanoscale distances from changes in the non-radiative transfer of energy between donor and acceptor fluorophores. For macromolecules and complexes this observed transfer efficiency is used to infer changes in molecular conformation under differing experimental conditions. However, sometimes shifts are observed in the FRET efficiency even when there is strong experimental evidence that the molecular conformational state is unchanged. We investigate ways in which such discrepancies can arise from kinetic effects. We show that significant shifts can arise from the interplay between excitation kinetics, orientation diffusion of fluorophores, separation diffusion of fluorophores, and non-emitting quenching.

  10. Investigation on ionic states of 1,2-Dipalmitoyl-sn-glycero-3-phosphorylcholine (DPPC) using organic laser dyes: A FRET study

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Arpan Datta; Saha, Jaba; Dey, D.; Bhattacharjee, D.; Hussain, Syed Arshad, E-mail: sa_h153@hotmail.com

    2017-05-15

    Fluorescence Resonance Energy Transfer (FRET) between two organic dyes Fluorescein and Rhodamine 6G were successfully investigated in aqueous solution in presence and absence of 1,2-Dipalmitoyl-sn-glycero-3-phosphorylcholine (DPPC) at different pH. Spectroscopic studies suggest that both the dyes were present mainly as monomer in solution. FRET occurred from Fluorescein to Rhodamine 6G in solutions. Energy transfer efficiency increases in presence of DPPC and the maximum efficiency was 59.3% when the concentration of DPPC was 1.4×10{sup −4} M at ambient condition. pH plays a crucial role in this investigation as the energy transfer efficiency was found to change in presence of DPPC at different pH. It has been demonstrated that with proper calibration it is possible to use the present system under investigation to realize various ionic states of DPPC by observing the change in FRET efficiency between these two dyes. - Graphical abstract: Electrostatic interaction between anionic Flu and cationic R6G molecules in presence and absence of DPPC at different pH. Here pH of DPPC was changed, not the pH of individual dyes.

  11. Neural correlates of creativity in analogical reasoning.

    Science.gov (United States)

    Green, Adam E; Kraemer, David J M; Fugelsang, Jonathan A; Gray, Jeremy R; Dunbar, Kevin N

    2012-03-01

    Brain-based evidence has implicated the frontal pole of the brain as important for analogical mapping. Separately, cognitive research has identified semantic distance as a key determinant of the creativity of analogical mapping (i.e., more distant analogies are generally more creative). Here, we used functional magnetic resonance imaging to assess brain activity during an analogy generation task in which we varied the semantic distance of analogical mapping (as derived quantitatively from a latent semantic analysis). Data indicated that activity within an a priori region of interest in left frontopolar cortex covaried parametrically with increasing semantic distance, even after removing effects of task difficulty. Results implicate increased recruitment of frontopolar cortex as a mechanism for integrating semantically distant information to generate solutions in creative analogical reasoning. 2012 APA, all rights reserved

  12. An entropy-based improved k-top scoring pairs (TSP) method for ...

    African Journals Online (AJOL)

    An entropy-based improved k-top scoring pairs (TSP) (Ik-TSP) method was presented in this study for the classification and prediction of human cancers based on gene-expression data. We compared Ik-TSP classifiers with 5 different machine learning methods and the k-TSP method based on 3 different feature selection ...

  13. Automatic Generation of Analogy Questions for Student Assessment: An Ontology-Based Approach

    Science.gov (United States)

    Alsubait, Tahani; Parsia, Bijan; Sattler, Uli

    2012-01-01

    Different computational models for generating analogies of the form "A is to B as C is to D" have been proposed over the past 35 years. However, analogy generation is a challenging problem that requires further research. In this article, we present a new approach for generating analogies in Multiple Choice Question (MCQ) format that can be used…

  14. How Analogy Drives Physics

    International Nuclear Information System (INIS)

    Hofstadter, Doug

    2004-01-01

    Many new ideas in theoretical physics come from analogies to older ideas in physics. For instance, the abstract notion of 'isospin' (or isotopic spin) originated in the prior concept of 'spin' (quantized angular momentum); likewise, the concept of 'phonon' (quantum of sound, or quantized collective excitation of a crystal) was based on the prior concept of 'photon' (quantum of light, or quantized element of the electromagnetic field). But these two examples, far from being exceptions, in fact represent the bread and butter of inventive thinking in physics. In a nutshell, intraphysics analogy-making -- borrowing by analogy with something already known in another area of physics -- is central to the progress of physics. The aim of this talk is to reveal the pervasiveness -- indeed, the indispensability -- of this kind of semi-irrational, wholly intuitive type of thinking (as opposed to more deductive mathematical inference) in the mental activity known as 'doing physics'. Speculations as to why wild analogical leaps are so crucial to the act of discovery in physics (as opposed to other disciplines) will be offered.

  15. Development of a pan-Babesia FRET-qPCR and a survey of livestock from five Caribbean islands.

    Science.gov (United States)

    Li, Jing; Kelly, Patrick; Zhang, Jilei; Xu, Chuanling; Wang, Chengming

    2015-09-30

    Babesia spp. are tick-borne protozoan hemoparasites and the second most common blood-borne parasites of mammals, in particular domestic animals. We used the Clustal Multiple Alignment program and 18S rRNA gene sequences of 22 Babesia species from GenBank to develop a PCR that could detect a wide variety of Babesia spp. in a single reaction. The pan-Babesia FRET-qPCR we developed reliably detected B. gibsoni, B. canis, B. vogeli, B. microti, B. bovis, and B. divergens under controlled conditions but did not react with closely related species, mainly Hepatozoon americanum, Theileria equi, and Toxoplasma gondii. When we tested the pan-Babesia FRET-qPCR on DNA of whole blood from 752 cattle, sheep, goats, donkeys and horses from five Caribbean islands, we detected Babesia spp. expected to be present in the animals, mainly B. bovis and B. bigemina in cattle and B. caballi in horses and donkeys. Further, we found that animals were not uncommonly infected with species of Babesia usually associated with other hosts, mainly B. vogeli and B. gibsoni in cattle, sheep and goats, B. rossi in goats, and B. caballi in goats and sheep. Finally, the pan-Babesia FRET-qPCR enabled us to identify unknown species of Babesia in cattle, goats, sheep and donkeys. Overall, 70 % (525/752) of the animals we tested were positive confirming earlier limited studies that infections with Babesia spp. are common in livestock in the Caribbean.

  16. Characterization of a spectrally diverse set of fluorescent proteins as FRET acceptors for mTurquoise2

    NARCIS (Netherlands)

    Mastop, M.; Bindels, D.S.; Shaner, N.C.; Postma, M.; Gadella, T.W.J.; Goedhart, J.

    2017-01-01

    The performance of Förster Resonance Energy Transfer (FRET) biosensors depends on brightness and photostability, which are dependent on the characteristics of the fluorescent proteins that are employed. Yellow fluorescent protein (YFP) is often used as an acceptor but YFP is prone to photobleaching

  17. Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide.

    Science.gov (United States)

    Pramanik, Smritimoy; Nakamura, Kaori; Usui, Kenji; Nakano, Shu-ichi; Saxena, Sarika; Matsui, Jun; Miyoshi, Daisuke; Sugimoto, Naoki

    2011-03-14

    We found that Hoogsteen base pairs were stabilized by molecular crowding and a histone H3-mimicking peptide, which was not observed for Watson-Crick base pairs. Our findings demonstrate that the type of DNA base pair is critical for the interaction between DNA and histones.

  18. Inter-Dye Distance Distributions Studied by a Combination of Single-Molecule FRET-Filtered Lifetime Measurements and a Weighted Accessible Volume (wAV Algorithm

    Directory of Open Access Journals (Sweden)

    Henning Höfig

    2014-11-01

    Full Text Available Förster resonance energy transfer (FRET is an important tool for studying the structural and dynamical properties of biomolecules. The fact that both the internal dynamics of the biomolecule and the movements of the biomolecule-attached dyes can occur on similar timescales of nanoseconds is an inherent problem in FRET studies. By performing single-molecule FRET-filtered lifetime measurements, we are able to characterize the amplitude of the motions of fluorescent probes attached to double-stranded DNA standards by means of flexible linkers. With respect to previously proposed experimental approaches, we improved the precision and the accuracy of the inter-dye distance distribution parameters by filtering out the donor-only population with pulsed interleaved excitation. A coarse-grained model is employed to reproduce the experimentally determined inter-dye distance distributions. This approach can easily be extended to intrinsically flexible proteins allowing, under certain conditions, to decouple the macromolecule amplitude of motions from the contribution of the dye linkers.

  19. Watson-Crick base pairing controls excited-state decay in natural DNA.

    Science.gov (United States)

    Bucher, Dominik B; Schlueter, Alexander; Carell, Thomas; Zinth, Wolfgang

    2014-10-13

    Excited-state dynamics are essential to understanding the formation of DNA lesions induced by UV light. By using femtosecond IR spectroscopy, it was possible to determine the lifetimes of the excited states of all four bases in the double-stranded environment of natural DNA. After UV excitation of the DNA duplex, we detected a concerted decay of base pairs connected by Watson-Crick hydrogen bonds. A comparison of single- and double-stranded DNA showed that the reactive charge-transfer states formed in the single strands are suppressed by base pairing in the duplex. The strong influence of the Watson-Crick hydrogen bonds indicates that proton transfer opens an efficient decay path in the duplex that prohibits the formation or reduces the lifetime of reactive charge-transfer states. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Automatic activation of categorical and abstract analogical relations in analogical reasoning.

    Science.gov (United States)

    Green, Adam E; Fugelsang, Jonathan A; Dunbar, Kevin N

    2006-10-01

    We examined activation of concepts during analogical reasoning. Subjects made either analogical judgments or categorical judgments about four-word sets. After each four-word set, they named the ink color of a single word in a modified Stroop task. Words that referred to category relations were primed (as indicated by longer response times on Stroop color naming) subsequent to analogical judgments and categorical judgments. This finding suggests that activation of category concepts plays a fundamental role in analogical thinking. When colored words referred to analogical relations, priming occurred subsequent to analogical judgments, but not to categorical judgments, even though identical four-word stimuli were used for both types of judgments. This finding lends empirical support to the hypothesis that, when people comprehend the analogy between two items, they activate an abstract analogical relation that is distinct from the specific content items that compose the analogy.

  1. Protein A Detection Based on Quantum Dots-Antibody Bioprobe Using Fluorescence Coupled Capillary Electrophoresis

    Directory of Open Access Journals (Sweden)

    Lin Qiu

    2014-01-01

    Full Text Available In this report, fluorescence detection coupled capillary electrophoresis (CE-FL was used to detect Protein A. Antibody was first labeled with Cy5 and then mixed with quantum dots (QDs to form QDs-antibody bioprobe. Further, we observed fluorescence resonance energy transfer (FRET from QDs donor to Cy5 acceptor. The bioprobe was formed and brought QDs and Cy5 close enough to allow FRET to occur. After adding protein A, the FRET system was broken and caused the FRET signal to decrease. Thus, a new method for the determination of protein A was proposed based on the FRET signal changes. This study provides a new trail of thought for the detection of protein.

  2. Analog series-based scaffolds: computational design and exploration of a new type of molecular scaffolds for medicinal chemistry

    Science.gov (United States)

    Dimova, Dilyana; Stumpfe, Dagmar; Hu, Ye; Bajorath, Jürgen

    2016-01-01

    Aim: Computational design of and systematic search for a new type of molecular scaffolds termed analog series-based scaffolds. Materials & methods: From currently available bioactive compounds, analog series were systematically extracted, key compounds identified and new scaffolds isolated from them. Results: Using our computational approach, more than 12,000 scaffolds were extracted from bioactive compounds. Conclusion: A new scaffold definition is introduced and a computational methodology developed to systematically identify such scaffolds, yielding a large freely available scaffold knowledge base. PMID:28116132

  3. Hairpin-like fluorescent probe for imaging of NF-κB transcription factor activity.

    Science.gov (United States)

    Metelev, Valeri; Zhang, Surong; Tabatadze, David; Bogdanov, Alexei

    2011-04-20

    Three oligodeoxyribonucleotides (ODN) covalently labeled with near-infrared (NIR) fluorochromes were synthesized and characterized with a goal of comparing in vitro a hairpin-based and a duplex-based FRET probe designed for the detection of human recombinant NF-κB p50/p65 heterodimer binding to DNA. Using deoxyguanosine phosphoramidite with a phosphorus-linked aminoethylene (diethylene glycol) hydrophilic linker, we synthesized ODNs with internucleoside reactive sites. The hairpin loop amino linker was modified with IRDye 800CW (FRET acceptor), and the 3'-end was modified with Cy5.5 (FRET donor) using a dithio-linker. To obtain a duplex probe, we conjugated Cy5.5 and 800CW to complementary strands at the distance of ten base pairs in the resultant duplex. No quenching of dyes was observed in either probe. The FRET efficiency was higher in the duplex (71%) than in the hairpin (56%) due to a more favorable distance between the donor and the acceptor. However, the hairpin design allowed more precise ratiometric measurement of fluorescence intensity changes as a result of NF-κB p50/p65 binding to the probe. We determined that as a result of binding there was a statistically significant increase of fluorescence intensity of Cy5.5 (donor) due to a decrease of FRET if normalized by 800CW intensity measured independently of FRET. We conclude that the hairpin based probe design allows for the synthesis of a dual fluorescence imaging probe that renders signal changes that are simple to interpret and stoichiometrically correct for detecting transcription factor-DNA interactions.

  4. Toward Wireless Health Monitoring via an Analog Signal Compression-Based Biosensing Platform.

    Science.gov (United States)

    Zhao, Xueyuan; Sadhu, Vidyasagar; Le, Tuan; Pompili, Dario; Javanmard, Mehdi

    2018-06-01

    Wireless all-analog biosensor design for the concurrent microfluidic and physiological signal monitoring is presented in this paper. The key component is an all-analog circuit capable of compressing two analog sources into one analog signal by the analog joint source-channel coding (AJSCC). Two circuit designs are discussed, including the stacked-voltage-controlled voltage source (VCVS) design with the fixed number of levels, and an improved design, which supports a flexible number of AJSCC levels. Experimental results are presented on the wireless biosensor prototype, composed of printed circuit board realizations of the stacked-VCVS design. Furthermore, circuit simulation and wireless link simulation results are presented on the improved design. Results indicate that the proposed wireless biosensor is well suited for sensing two biological signals simultaneously with high accuracy, and can be applied to a wide variety of low-power and low-cost wireless continuous health monitoring applications.

  5. Performance of various density functionals for the hydrogen bonds in DNA base pairs

    NARCIS (Netherlands)

    van der Wijst, T.; Fonseca Guerra, C.; Swart, M.; Bickelhaupt, F.M.

    2006-01-01

    We have investigated the performance of seven popular density functionals (B3LYP, BLYP, BP86, mPW, OPBE, PBE, PW91) for describing the geometry and stability of the hydrogen bonds in DNA base pairs. For the gas-phase situation, the hydrogen-bond lengths and strengths in the DNA pairs have been

  6. An analog VLSI real time optical character recognition system based on a neural architecture

    International Nuclear Information System (INIS)

    Bo, G.; Caviglia, D.; Valle, M.

    1999-01-01

    In this paper a real time Optical Character Recognition system is presented: it is based on a feature extraction module and a neural network classifier which have been designed and fabricated in analog VLSI technology. Experimental results validate the circuit functionality. The results obtained from a validation based on a mixed approach (i.e., an approach based on both experimental and simulation results) confirm the soundness and reliability of the system

  7. An analog VLSI real time optical character recognition system based on a neural architecture

    Energy Technology Data Exchange (ETDEWEB)

    Bo, G.; Caviglia, D.; Valle, M. [Genoa Univ. (Italy). Dip. of Biophysical and Electronic Engineering

    1999-03-01

    In this paper a real time Optical Character Recognition system is presented: it is based on a feature extraction module and a neural network classifier which have been designed and fabricated in analog VLSI technology. Experimental results validate the circuit functionality. The results obtained from a validation based on a mixed approach (i.e., an approach based on both experimental and simulation results) confirm the soundness and reliability of the system.

  8. A low power low noise analog front end for portable healthcare system

    International Nuclear Information System (INIS)

    Wang Yanchao; Ke Keren; Qin Wenhui; Qin Yajie; Yi Ting; Hong Zhiliang

    2015-01-01

    The presented analog front end (AFE) used to process human bio-signals consists of chopping instrument amplifier (IA), chopping spikes filter and programmable gain and bandwidth amplifier. The capacitor-coupling input of AFE can reject the DC electrode offset. The power consumption of current-feedback based IA is reduced by adopting capacitor divider in the input and feedback network. Besides, IA's input thermal noise is decreased by utilizing complementary CMOS input pairs which can offer higher transconductance. Fabricated in Global Foundry 0.35 μm CMOS technology, the chip consumes 3.96 μA from 3.3 V supply. The measured input noise is 0.85 μVrms (0.5–100 Hz) and the achieved noise efficient factor is 6.48. (paper)

  9. Development and validation of an app-based cell counter for use in the clinical laboratory setting

    Directory of Open Access Journals (Sweden)

    Alexander C Thurman

    2015-01-01

    Full Text Available Introduction: For decades cellular differentials have been generated exclusively on analog tabletop cell counters. With the advent of tablet computers, digital cell counters - in the form of mobile applications ("apps" - now represent an alternative to analog devices. However, app-based counters have not been widely adopted by clinical laboratories, perhaps owing to a presumed decrease in count accuracy related to the lack of tactile feedback inherent in a touchscreen interface. We herein provide the first systematic evidence that digital cell counters function similarly to standard tabletop units. Methods: We developed an app-based cell counter optimized for use in the clinical laboratory setting. Paired counts of 188 peripheral blood smears and 62 bone marrow aspirate smears were performed using our app-based counter and a standard analog device. Differences between paired data sets were analyzed using the correlation coefficient, Student′s t-test for paired samples and Bland-Altman plots. Results: All counts showed excellent agreement across all users and touch screen devices. With the exception of peripheral blood basophils (r = 0.684, differentials generated for the measured cell categories within the paired data sets were highly correlated (all r ≥ 0.899. Results of paired t-tests did not reach statistical significance for any cell type (all P > 0.05, and Bland-Altman plots showed a narrow spread of the difference about the mean without evidence of significant outliers. Conclusions: Our analysis suggests that no systematic differences exist between cellular differentials obtained via app-based or tabletop counters and that agreement between these two methods is excellent.

  10. Computational design of new molecular scaffolds for medicinal chemistry, part II: generalization of analog series-based scaffolds

    Science.gov (United States)

    Dimova, Dilyana; Stumpfe, Dagmar; Bajorath, Jürgen

    2018-01-01

    Aim: Extending and generalizing the computational concept of analog series-based (ASB) scaffolds. Materials & methods: Methodological modifications were introduced to further increase the coverage of analog series (ASs) and compounds by ASB scaffolds. From bioactive compounds, ASs were systematically extracted and second-generation ASB scaffolds isolated. Results: More than 20,000 second-generation ASB scaffolds with single or multiple substitution sites were extracted from active compounds, achieving more than 90% coverage of ASs. Conclusion: Generalization of the ASB scaffold approach has yielded a large knowledge base of scaffold-capturing compound series and target information. PMID:29379641

  11. Analog computing

    CERN Document Server

    Ulmann, Bernd

    2013-01-01

    This book is a comprehensive introduction to analog computing. As most textbooks about this powerful computing paradigm date back to the 1960s and 1970s, it fills a void and forges a bridge from the early days of analog computing to future applications. The idea of analog computing is not new. In fact, this computing paradigm is nearly forgotten, although it offers a path to both high-speed and low-power computing, which are in even more demand now than they were back in the heyday of electronic analog computers.

  12. RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

    Science.gov (United States)

    Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

    2017-02-01

    Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

  13. Stabilization of Nucleosomes by Histone Tails and by FACT Revealed by spFRET Microscopy

    Directory of Open Access Journals (Sweden)

    Maria E. Valieva

    2017-01-01

    Full Text Available A correct chromatin structure is important for cell viability and is tightly regulated by numerous factors. Human protein complex FACT (facilitates chromatin transcription is an essential factor involved in chromatin transcription and cancer development. Here FACT-dependent changes in the structure of single nucleosomes were studied with single-particle Förster resonance energy transfer (spFRET microscopy using nucleosomes labeled with a donor-acceptor pair of fluorophores, which were attached to the adjacent gyres of DNA near the contact between H2A-H2B dimers. Human FACT and its version without the C-terminal domain (CTD and the high mobility group (HMG domain of the structure-specific recognition protein 1 (SSRP1 subunit did not change the structure of the nucleosomes, while FACT without the acidic C-terminal domains of the suppressor of Ty 16 (Spt16 and the SSRP1 subunits caused nucleosome aggregation. Proteolytic removal of histone tails significantly disturbed the nucleosome structure, inducing partial unwrapping of nucleosomal DNA. Human FACT reduced DNA unwrapping and stabilized the structure of tailless nucleosomes. CTD and/or HMG domains of SSRP1 are required for this FACT activity. In contrast, previously it has been shown that yeast FACT unfolds (reorganizes nucleosomes using the CTD domain of SSRP1-like Pol I-binding protein 3 subunit (Pob3. Thus, yeast and human FACT complexes likely utilize the same domains for nucleosome reorganization and stabilization, respectively, and these processes are mechanistically similar.

  14. Aviram–Ratner rectifying mechanism for DNA base-pair sequencing through graphene nanogaps

    International Nuclear Information System (INIS)

    Agapito, Luis A; Gayles, Jacob; Wolowiec, Christian; Kioussis, Nicholas

    2012-01-01

    We demonstrate that biological molecules such as Watson–Crick DNA base pairs can behave as biological Aviram–Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab initio non-equilibrium Green’s function (NEGF) theory to determine the electrical response of graphene—base-pair—graphene junctions. The results show an asymmetric (rectifying) current–voltage response for the cytosine–guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the thymine–adenine case. We propose applying the asymmetry of the current–voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps. (paper)

  15. Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

    International Nuclear Information System (INIS)

    Torigoe, Hidetaka; Miyakawa, Yukako; Ono, Akira; Kozasa, Tetsuo

    2012-01-01

    Highlights: ► Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio. ► The binding constant between Hg 2+ and the T:T mismatched base pair was 10 6 M −1 . ► The binding constant was larger than those for nonspecific metal–DNA interactions. ► The binding constant for the second Hg 2+ was larger than that for the first Hg 2+ . ► The positive cooperative binding was observed between Hg 2+ and multiple T:T. - Abstract: Metal-mediated base pairs by the interaction between metal ions and artificial bases in oligonucleotides have been developed for their potential applications in nanotechnology. We recently found that a natural T:T mismatched base pair bound with Hg 2+ ion to form a novel T–Hg–T base pair. Here, we examined the thermodynamic properties of the binding between Hg 2+ and each of the single and double T:T mismatched base pair duplex DNAs by isothermal titration calorimetry. Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio with 10 6 M −1 binding constant, which was significantly larger than those for nonspecific metal ion–DNA interactions. In the Hg 2+ –double T:T mismatched base pair interaction, the affinity for the second Hg 2+ binding was significantly larger than that for the first Hg 2+ binding. The positively cooperative binding may be favorable to align multiple Hg 2+ in duplex DNA for the application of the metal-mediated base pairs in nanotechnology.

  16. Sub-ensemble monitoring of DNA strand displacement using multiparameter single-molecule FRET

    OpenAIRE

    Baltierra Jasso, Laura; Morten, Michael; Magennis, Steven William

    2018-01-01

    Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constan...

  17. A Physical Analog Model of Strike-Slip Faulting for Model-Based Inquiry in the Classroom

    Science.gov (United States)

    Curren, I. S.; Glesener, G.

    2013-12-01

    classroom setting. We hope to encourage discussion from session attendees on the use of physical analog models and real-time quantitative model-based inquiry in the development of the next generation of geoscientists.

  18. Source selection for analogical reasoning an empirical approach

    Energy Technology Data Exchange (ETDEWEB)

    Stubblefield, W.A. [Sandia National Labs., Albuquerque, NM (United States); Luger, G.F. [Univ. of New Mexico, Albuquerque, NM (United States)

    1996-12-31

    The effectiveness of an analogical reasoner depends upon its ability to select a relevant analogical source. In many problem domains, however, too little is known about target problems to support effective source selection. This paper describes the design and evaluation of SCAVENGER, an analogical reasoner that applies two techniques to this problem: (1) An assumption-based approach to matching that allows properties of candidate sources to match unknown target properties in the absence of evidence to the contrary. (2) The use of empirical learning to improve memory organization based on problem solving experience.

  19. The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.

    Science.gov (United States)

    Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul

    2013-06-17

    Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Visualizing RNA Secondary Structure Base Pair Binding Probabilities using Nested Concave Hulls

    OpenAIRE

    Sansen , Joris; Bourqui , Romain; Thebault , Patricia; Allali , Julien; Auber , David

    2015-01-01

    International audience; The challenge 1 of the BIOVIS 2015 design contest consists in designing an intuitive visual depiction of base pairs binding probabilities for secondary structure of ncRNA. Our representation depicts the potential nucleotide pairs binding using nested concave hulls over the computed MFE ncRNA secondary structure. Thus, it allows to identify regions with a high level of uncertainty in the MFE computation and the structures which seem to match to reality.

  1. A fast multichannel analog storage system

    International Nuclear Information System (INIS)

    Freytag, D.R.

    1983-01-01

    A Multichannel Analog Storage System based on a commercial 32-channel parallel in/serial out (PISO) analog shift register is described. The basic unit is a single width CAMAC module containing 512 analog cells and the associated logic for data storage and subsequent readout. At sampling rates of up to 30 MHz the signals are strobed directly into the PISO. At higher rates signals are strobed into a fast presampling stage and subsequently transferred in block form into an array of PISO's. Sampling rates of 300 MHz have been achieved with the present device and 1000 MHz are possible with improved signal drivers. The system is well suited for simultaneous handling of many signal channels with moderate numbers of samples in each channel. RMS noise over full scale signal has been measured as 1:3000 (approx. =11 bit). However, nonlinearities in the response and differences in sensitivity of the analog cells require an elaborate calibration system in order to realize 11 bit accuracy for the analog information

  2. Regulatory assembly of the vacuolar proton pump VoV1-ATPase in yeast cells by FLIM-FRET

    Science.gov (United States)

    Ernst, Stefan; Batisse, Claire; Zarrabi, Nawid; Böttcher, Bettina; Börsch, Michael

    2010-02-01

    We investigate the reversible disassembly of VOV1-ATPase in life yeast cells by time resolved confocal FRET imaging. VOV1-ATPase in the vacuolar membrane pumps protons from the cytosol into the vacuole. VOV1-ATPase is a rotary biological nanomotor driven by ATP hydrolysis. The emerging proton gradient is used for secondary transport processes as well as for pH and Ca2+ homoeostasis in the cell. The activity of the VOV1-ATPase is regulated through assembly / disassembly processes. During starvation the two parts of VOV1-ATPase start to disassemble. This process is reversed after addition of glucose. The exact mechanisms are unknown. To follow the disassembly / reassembly in vivo we tagged two subunits C and E with different fluorescent proteins. Cellular distributions of C and E were monitored using a duty cycle-optimized alternating laser excitation scheme (DCO-ALEX) for time resolved confocal FRET-FLIM measurements.

  3. Amperean Pairing and the Pseudogap Phase of Cuprate Superconductors

    Science.gov (United States)

    Lee, Patrick A.

    2014-07-01

    The enigmatic pseudogap phase in underdoped cuprate high-Tc superconductors has long been recognized as a central puzzle of the Tc problem. Recent data show that the pseudogap is likely a distinct phase, characterized by a medium range and quasistatic charge ordering. However, the origin of the ordering wave vector and the mechanism of the charge order is unknown. At the same time, earlier data show that precursive superconducting fluctuations are also associated with this phase. We propose that the pseudogap phase is a novel pairing state where electrons on the same side of the Fermi surface are paired, in strong contrast with conventional Bardeen-Cooper-Schrieffer theory which pairs electrons on opposite sides of the Fermi surface. In this state the Cooper pair carries a net momentum and belongs to a general class called pair density wave. The microscopic pairing mechanism comes from a gauge theory formulation of the resonating valence bond (RVB) picture, where spinons traveling in the same direction feel an attractive force in analogy with Ampere's effects in electromagnetism. We call this Amperean pairing. Charge order automatically appears as a subsidiary order parameter even when long-range pair order is destroyed by phase fluctuations. Our theory gives a prediction of the ordering wave vector which is in good agreement with experiment. Furthermore, the quasiparticle spectrum from our model explains many of the unusual features reported in photoemission experiments. The Fermi arc, the unusual way the tip of the arc terminates, and the relation of the spanning vector of the arc tips to the charge ordering wave vector also come out naturally. Finally, we propose an experiment that can directly test the notion of Amperean pairing.

  4. VHDL-based programming environment for Floating-Gate analog memory cell

    Directory of Open Access Journals (Sweden)

    Carlos Alberto dos Reis Filho

    2005-02-01

    Full Text Available An implementation in CMOS technology of a Floating-Gate Analog Memory Cell and Programming Environment is presented. A digital closed-loop control compares a reference value set by user and the memory output and after cycling, the memory output is updated and the new value stored. The circuit can be used as analog trimming for VLSI applications where mechanical trimming associated with postprocessing chip is prohibitive due to high costs.

  5. Base-pairing preferences, physicochemical properties and mutational behaviour of the DNA lesion 8-nitroguanine.

    Science.gov (United States)

    Bhamra, Inder; Compagnone-Post, Patricia; O'Neil, Ian A; Iwanejko, Lesley A; Bates, Andrew D; Cosstick, Richard

    2012-11-01

    8-Nitro-2'-deoxyguanosine (8-nitrodG) is a relatively unstable, mutagenic lesion of DNA that is increasingly believed to be associated with tissue inflammation. Due to the lability of the glycosidic bond, 8-nitrodG cannot be incorporated into oligodeoxynucleotides (ODNs) by chemical DNA synthesis and thus very little is known about its physicochemical properties and base-pairing preferences. Here we describe the synthesis of 8-nitro-2'-O-methylguanosine, a ribonucleoside analogue of this lesion, which is sufficiently stable to be incorporated into ODNs. Physicochemical studies demonstrated that 8-nitro-2'-O-methylguanosine adopts a syn conformation about the glycosidic bond; thermal melting studies and molecular modelling suggest a relatively stable syn-8-nitroG·anti-G base pair. Interestingly, when this lesion analogue was placed in a primer-template system, extension of the primer by either avian myeloblastosis virus reverse transcriptase (AMV-RT) or human DNA polymerase β (pol β), was significantly impaired, but where incorporation opposite 8-nitroguanine did occur, pol β showed a 2:1 preference to insert dA over dC, while AMV-RT incorporated predominantly dC. The fact that no 8-nitroG·G base pairing is seen in the primer extension products suggests that the polymerases may discriminate against this pairing system on the basis of its poor geometric match to a Watson-Crick pair.

  6. Base-pairing preferences, physicochemical properties and mutational behaviour of the DNA lesion 8-nitroguanine†

    Science.gov (United States)

    Bhamra, Inder; Compagnone-Post, Patricia; O’Neil, Ian A.; Iwanejko, Lesley A.; Bates, Andrew D.; Cosstick, Richard

    2012-01-01

    8-Nitro-2′-deoxyguanosine (8-nitrodG) is a relatively unstable, mutagenic lesion of DNA that is increasingly believed to be associated with tissue inflammation. Due to the lability of the glycosidic bond, 8-nitrodG cannot be incorporated into oligodeoxynucleotides (ODNs) by chemical DNA synthesis and thus very little is known about its physicochemical properties and base-pairing preferences. Here we describe the synthesis of 8-nitro-2′-O-methylguanosine, a ribonucleoside analogue of this lesion, which is sufficiently stable to be incorporated into ODNs. Physicochemical studies demonstrated that 8-nitro-2′-O-methylguanosine adopts a syn conformation about the glycosidic bond; thermal melting studies and molecular modelling suggest a relatively stable syn-8-nitroG·anti-G base pair. Interestingly, when this lesion analogue was placed in a primer-template system, extension of the primer by either avian myeloblastosis virus reverse transcriptase (AMV-RT) or human DNA polymerase β (pol β), was significantly impaired, but where incorporation opposite 8-nitroguanine did occur, pol β showed a 2:1 preference to insert dA over dC, while AMV-RT incorporated predominantly dC. The fact that no 8-nitroG·G base pairing is seen in the primer extension products suggests that the polymerases may discriminate against this pairing system on the basis of its poor geometric match to a Watson–Crick pair. PMID:22965127

  7. Flow-induced vibration and fretting-wear specifications to ensure steam-generator and heat exchanger lifetime performance

    International Nuclear Information System (INIS)

    Janzen, V.P.; Han, Y.; Pettigrew, M.J.

    2008-01-01

    The current interest in refurbishment, life extension and new-build activity has meant a renewed emphasis on technical specifications that will ensure improved reliability and longer life. Preventing vibration and fretting-wear problems in steam generators and heat exchangers requires design specifications that bring together specific guidelines, analysis methods, requirements and appropriate performance criteria. The specifications must be firmly based on experimental data and field inspections. In addition, the specifications must be supported by theoretical analyses and fundamental scaling correlations, to cover conditions and geometries over the wide range applicable to existing components and probable future designs. The specifications are expected to evolve to meet changing industry requirements. This paper outlines the steps required to generate and support design specifications, and relates them to typical steam-generator design features and computer modeling capabilities. It also describes current issues that are driving changes to flow-induced vibration and fretting-wear specifications that can be applied to the design process for component refurbishment, replacement or new designs. These issues include recent experimental or field evidence for new excitation mechanisms, e.g., the possibility of in-plane fluidelastic instability of U-tubes, the demand for longer reactor and component lifetimes, the need for better predictions of dynamic properties and vibration response, e.g., two-phase random-turbulence excitation, and requirements to consider system 'excursions' or abnormal scenarios, e.g., a main steam line break in the case of steam generators. The paper describes steps being taken to resolve these issues. (author)

  8. Communication disruption of guava moth (Coscinoptycha improbana) using a pheromone analog based on chain length.

    Science.gov (United States)

    Suckling, D M; Dymock, J J; Park, K C; Wakelin, R H; Jamieson, L E

    2013-09-01

    The guava moth, Coscinoptycha improbana, an Australian species that infests fruit crops in commercial and home orchards, was first detected in New Zealand in 1997. A four-component pheromone blend was identified but is not yet commercially available. Using single sensillum recordings from male antennae, we established that the same olfactory receptor neurons responded to two guava moth sex pheromone components, (Z)-11-octadecen-8-one and (Z)-12-nonadecen-9-one, and to a chain length analog, (Z)-13-eicosen-10-one, the sex pheromone of the related peach fruit moth, Carposina sasakii. We then field tested whether this non-specificity of the olfactory neurons might enable disruption of sexual communication by the commercially available analog, using male catch to synthetic lures in traps in single-tree, nine-tree and 2-ha plots. A disruptive pheromone analog, based on chain length, is reported for the first time. Trap catches for guava moth were disrupted by three polyethylene tubing dispensers releasing the analog in single-tree plots (86% disruption of control catches) and in a plots of nine trees (99% disruption). Where peach fruit moth pheromone dispensers were deployed at a density of 1000/ha in two 2-ha areas, pheromone traps for guava moth were completely disrupted for an extended period (up to 470 days in peri-urban gardens in Mangonui and 422 days in macadamia nut orchards in Kerikeri). In contrast, traps in untreated areas over 100 m away caught 302.8 ± 128.1 moths/trap in Mangonui and 327.5 ± 78.5 moths/ trap in Kerikeri. The longer chain length in the pheromone analog has greater longevity than the natural pheromone due to its lower volatility. Chain length analogs may warrant further investigation for mating disruption in Lepidoptera, and screening using single-sensillum recording is recommended.

  9. Science Teachers' Analogical Reasoning

    Science.gov (United States)

    Mozzer, Nilmara Braga; Justi, Rosária

    2013-08-01

    Analogies can play a relevant role in students' learning. However, for the effective use of analogies, teachers should not only have a well-prepared repertoire of validated analogies, which could serve as bridges between the students' prior knowledge and the scientific knowledge they desire them to understand, but also know how to introduce analogies in their lessons. Both aspects have been discussed in the literature in the last few decades. However, almost nothing is known about how teachers draw their own analogies for instructional purposes or, in other words, about how they reason analogically when planning and conducting teaching. This is the focus of this paper. Six secondary teachers were individually interviewed; the aim was to characterize how they perform each of the analogical reasoning subprocesses, as well as to identify their views on analogies and their use in science teaching. The results were analyzed by considering elements of both theories about analogical reasoning: the structural mapping proposed by Gentner and the analogical mechanism described by Vosniadou. A comprehensive discussion of our results makes it evident that teachers' content knowledge on scientific topics and on analogies as well as their pedagogical content knowledge on the use of analogies influence all their analogical reasoning subprocesses. Our results also point to the need for improving teachers' knowledge about analogies and their ability to perform analogical reasoning.

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

    Directory of Open Access Journals (Sweden)

    Md Mehedi Hasan

    Full Text Available 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/.

  11. Modified friction factor correlation for CICC's based on a porous media analogy

    Science.gov (United States)

    Lewandowska, Monika; Bagnasco, Maurizio

    2011-09-01

    A modified correlation for the bundle friction factor in CICC's based on a porous media analogy is presented. The correlation is obtained by the analysis of the collected pressure drop data measured for 23 CICC's. The friction factors predicted by the proposed correlation are compared with those resulting from the pressure drop data for two CICC's measured recently using cryogenic helium in the SULTAN test facility at EPFL-CRPP.

  12. Induced Förster resonance energy transfer by encapsulation of DNA-scaffold based probes inside a plant virus based protein cage

    Science.gov (United States)

    de Ruiter, Mark V.; Overeem, Nico J.; Singhai, Gaurav; Cornelissen, Jeroen J. L. M.

    2018-05-01

    Insight into the assembly and disassembly of viruses can play a crucial role in developing cures for viral diseases. Specialized fluorescent probes can benefit the study of interactions within viruses, especially during cell studies. In this work, we developed a strategy based on Förster resonance energy transfer (FRET) to study the assembly of viruses without labeling the exterior of viruses. Instead, we exploit their encapsulation of nucleic cargo, using three different fluorescent ATTO dyes linked to single-stranded DNA oligomers, which are hybridised to a longer DNA strand. FRET is induced upon assembly of the cowpea chlorotic mottle virus, which forms monodisperse icosahedral particles of about 22 nm, thereby increasing the FRET efficiency by a factor of 8. Additionally, encapsulation of the dyes in virus-like particles induces a two-step FRET. When the formed constructs are disassembled, this FRET signal is fully reduced to the value before encapsulation. This reversible behavior makes the system a good probe for studying viral assembly and disassembly. It, furthermore, shows that multi-component supramolecular materials are stabilized in the confinement of a protein cage.

  13. Förster Resonance Energy Transfer (FRET) between Heterogeneously Distributed Probes: Application to Lipid Nanodomains and Pores

    Czech Academy of Sciences Publication Activity Database

    Šachl, Radek; Johansson, L. B. A.; Hof, Martin

    2012-01-01

    Roč. 13, č. 12 (2012), s. 16141-16156 E-ISSN 1422-0067 R&D Projects: GA ČR GAP208/10/1090; GA ČR GAP208/10/0376 Institutional support: RVO:61388955 Keywords : FRET * lipid domains * pores Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.464, year: 2012

  14. High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.

    Science.gov (United States)

    Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Saneyoshi, Hisao; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

    2015-11-02

    Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. SEAS: A simulated evolution approach for analog circuit synthesis

    NARCIS (Netherlands)

    Ning, Zhen-Qiu; Ning, Zhen-Qiu; Mouthaan, A.J.; Wallinga, Hans

    1991-01-01

    The authors present a simulated evolution approach for analog circuit synthesis based on an analogy with the natural selection process in biological environments and on the iterative improvements in solving engineering problems. A prototype framework based on this idea, called SEAS, has been

  16. Non-Watson Crick base pairs might stabilize RNA structural motifs in ...

    Indian Academy of Sciences (India)

    Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural ...

  17. Elevated Levels of DNA Strand Breaks Induced by a Base Analog in the Human Cell Line with the P32T ITPA Variant

    Science.gov (United States)

    Waisertreiger, Irina S.-R.; Menezes, Miriam R.; Randazzo, James; Pavlov, Youri I.

    2010-01-01

    Base analogs are powerful antimetabolites and dangerous mutagens generated endogenously by oxidative stress, inflammation, and aberrant nucleotide biosynthesis. Human inosine triphosphate pyrophosphatase (ITPA) hydrolyzes triphosphates of noncanonical purine bases (i.e., ITP, dITP, XTP, dXTP, or their mimic: 6-hydroxyaminopurine (HAP) deoxynucleoside triphosphate) and thus regulates nucleotide pools and protects cells from DNA damage. We demonstrate that the model purine base analog HAP induces DNA breaks in human cells and leads to elevation of levels of ITPA. A human polymorphic allele of the ITPA, 94C->A encodes for the enzyme with a P32T amino-acid change and leads to accumulation of nonhydrolyzed ITP. The polymorphism has been associated with adverse reaction to purine base-analog drugs. The level of both spontaneous and HAP-induced DNA breaks is elevated in the cell line with the ITPA P32T variant. The results suggested that human ITPA plays a pivotal role in the protection of DNA from noncanonical purine base analogs. PMID:20936128

  18. Elevated Levels of DNA Strand Breaks Induced by a Base Analog in the Human Cell Line with the P32T ITPA Variant

    Directory of Open Access Journals (Sweden)

    Irina S.-R. Waisertreiger

    2010-01-01

    Full Text Available Base analogs are powerful antimetabolites and dangerous mutagens generated endogenously by oxidative stress, inflammation, and aberrant nucleotide biosynthesis. Human inosine triphosphate pyrophosphatase (ITPA hydrolyzes triphosphates of noncanonical purine bases (i.e., ITP, dITP, XTP, dXTP, or their mimic: 6-hydroxyaminopurine (HAP deoxynucleoside triphosphate and thus regulates nucleotide pools and protects cells from DNA damage. We demonstrate that the model purine base analog HAP induces DNA breaks in human cells and leads to elevation of levels of ITPA. A human polymorphic allele of the ITPA, 94C->A encodes for the enzyme with a P32T amino-acid change and leads to accumulation of nonhydrolyzed ITP. The polymorphism has been associated with adverse reaction to purine base-analog drugs. The level of both spontaneous and HAP-induced DNA breaks is elevated in the cell line with the ITPA P32T variant. The results suggested that human ITPA plays a pivotal role in the protection of DNA from noncanonical purine base analogs.

  19. Analogy, an Alternative Model.
 Critics to the standard model of analogical problems solving and proposals for an alternative one

    Directory of Open Access Journals (Sweden)

    Ricardo A. Minervino

    2016-02-01

    Full Text Available The authors made an extension of Hofstadter‘s criticisms against the standard approach in analogical thinking represented by the structure-mapping theory of Gentner and the multiconstraint theory of Holyoak and Thagard. Based on this extension, they proposed a non-serial model of analogical problem solving. Against the standard approach, the model postulates that: (a people detect and evaluate differences between mapped elements before the subprocess of inference generation and consider them in order to control it, and (b properties of an element that explain why the element could fill a certain role in the base problem resolution (PERs play a crucial role in these detection and evaluation operations, and also in post-inferences subprocesses. An experiment showed that: (a people detect and evaluate the relevance of differences between mapped elements before inference generation, (b that they inhibit the generation of literal inferences when they face relevant differences, and (c that they stop the subprocess when they recognize insuperable ones. The results also showed that base PERs are reactivated at different moments of analogical transfer. The data obtained are incompatible with the standard theories of analogical thinking, which treat inference generation as a syntactic mechanism and exclude contextual semantic analysis from the study of analogy

  20. Color Memory: A Yang-Mills Analog of Gravitational Wave Memory

    Science.gov (United States)

    Pate, Monica; Raclariu, Ana-Maria; Strominger, Andrew

    2017-12-01

    A transient color flux across null infinity in classical Yang-Mills theory is considered. It is shown that a pair of test "quarks" initially in a color singlet generically acquire net color as a result of the flux. A nonlinear formula is derived for the relative color rotation of the quarks. For a weak color flux, the formula linearizes to the Fourier transform of the soft gluon theorem. This color memory effect is the Yang-Mills analog of the gravitational memory effect.