The Application of The Double Queue Asymmetric Gated Service Polling Control Theory in Intelligent Traffic System

Directory of Open Access Journals (Sweden)

Zhao Yi Fan

2016-01-01

Full Text Available paper presents a new use of double queues asymmetric gated service polling system in the intelligent traffic light control system.Usually there are more vehicles in main road than minor road,so there are more green light time be needed in the main road.From the computer simulation and theory analysis,we can find that the application of double queues asymmetric gated service polling theory in intelligent traffic system can balance intersections load and set suitable passing time for vehicles to assure the roads open.

Mlh1-Mlh3, a Meiotic Crossover and DNA Mismatch Repair Factor, Is a Msh2-Msh3-stimulated Endonuclease*

Science.gov (United States)

Rogacheva, Maria V.; Manhart, Carol M.; Chen, Cheng; Guarne, Alba; Surtees, Jennifer; Alani, Eric

2014-01-01

Crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. In Saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. These invasion intermediates are converted into double Holliday junctions and then resolved into crossovers that facilitate homolog segregation during Meiosis I. Work in yeast suggests that Msh4-Msh5 stabilizes invasion intermediates and double Holliday junctions, which are resolved into crossovers in steps requiring Sgs1 helicase, Exo1, and a putative endonuclease activity encoded by the DNA mismatch repair factor Mlh1-Mlh3. We purified Mlh1-Mlh3 and showed that it is a metal-dependent and Msh2-Msh3-stimulated endonuclease that makes single-strand breaks in supercoiled DNA. These observations support a direct role for an Mlh1-Mlh3 endonuclease activity in resolving recombination intermediates and in DNA mismatch repair. PMID:24403070

Output voltage calculations in double barrier magnetic tunnel junctions with asymmetric voltage behavior

KAUST Repository

Useinov, Arthur; Mryasov, Oleg; Kosel, Jü rgen

2011-01-01

In this paper we study the asymmetric voltage behavior (AVB) of the tunnel magnetoresistance (TMR) for single and double barrier magnetic tunnel junctions (MTJs) in range of a quasi-classical free electron model. Numerical calculations of the TMR

High Quality Plasmonic Sensors Based on Fano Resonances Created through Cascading Double Asymmetric Cavities

OpenAIRE

Zhang, Xiangao; Shao, Mingzhen; Zeng, Xiaoqi

2016-01-01

In this paper, a type of compact nanosensor based on a metal-insulator-metal structure is proposed and investigated through cascading double asymmetric cavities, in which their metal cores shift along different axis directions. The cascaded asymmetric structure exhibits high transmission and sharp Fano resonance peaks via strengthening the mutual coupling of the cavities. The research results show that with the increase of the symmetry breaking in the structure, the number of Fano resonances ...

Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering

KAUST Repository

Aouida, Mustapha

2015-07-30

The Cas9 endonuclease is used for genome editing applications in diverse eukaryotic species. A high frequency of off-target activity has been reported in many cell types, limiting its applications to genome engineering, especially in genomic medicine. Here, we generated a synthetic chimeric protein between the catalytic domain of the FokI endonuclease and the catalytically inactive Cas9 protein (fdCas9). A pair of guide RNAs (gRNAs) that bind to sense and antisense strands with a defined spacer sequence range can be used to form a catalytically active dimeric fdCas9 protein and generate double-strand breaks (DSBs) within the spacer sequence. Our data demonstrate an improved catalytic activity of the fdCas9 endonuclease, with a spacer range of 15–39 nucleotides, on surrogate reporters and genomic targets. Furthermore, we observed no detectable fdCas9 activity at known Cas9 off-target sites. Taken together, our data suggest that the fdCas9 endonuclease variant is a superior platform for genome editing applications in eukaryotic systems including mammalian cells.

Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering

KAUST Repository

Aouida, Mustapha; Eid, Ayman; Ali, Zahir; Cradick, Thomas; Lee, Ciaran; Deshmukh, Harshavardhan; Atef, Ahmed; Abu Samra, Dina Bashir Kamil; Gadhoum, Samah Zeineb; Merzaban, Jasmeen; Bao, Gang; Mahfouz, Magdy M.

2015-01-01

The Cas9 endonuclease is used for genome editing applications in diverse eukaryotic species. A high frequency of off-target activity has been reported in many cell types, limiting its applications to genome engineering, especially in genomic medicine. Here, we generated a synthetic chimeric protein between the catalytic domain of the FokI endonuclease and the catalytically inactive Cas9 protein (fdCas9). A pair of guide RNAs (gRNAs) that bind to sense and antisense strands with a defined spacer sequence range can be used to form a catalytically active dimeric fdCas9 protein and generate double-strand breaks (DSBs) within the spacer sequence. Our data demonstrate an improved catalytic activity of the fdCas9 endonuclease, with a spacer range of 15–39 nucleotides, on surrogate reporters and genomic targets. Furthermore, we observed no detectable fdCas9 activity at known Cas9 off-target sites. Taken together, our data suggest that the fdCas9 endonuclease variant is a superior platform for genome editing applications in eukaryotic systems including mammalian cells.

Divalent metal ion differentially regulates the sequential nicking reactions of the GIY-YIG homing endonuclease I-BmoI.

Directory of Open Access Journals (Sweden)

Benjamin P Kleinstiver

Full Text Available Homing endonucleases are site-specific DNA endonucleases that function as mobile genetic elements by introducing double-strand breaks or nicks at defined locations. Of the major families of homing endonucleases, the modular GIY-YIG endonucleases are least understood in terms of mechanism. The GIY-YIG homing endonuclease I-BmoI generates a double-strand break by sequential nicking reactions during which the single active site of the GIY-YIG nuclease domain must undergo a substantial reorganization. Here, we show that divalent metal ion plays a significant role in regulating the two independent nicking reactions by I-BmoI. Rate constant determination for each nicking reaction revealed that limiting divalent metal ion has a greater impact on the second strand than the first strand nicking reaction. We also show that substrate mutations within the I-BmoI cleavage site can modulate the first strand nicking reaction over a 314-fold range. Additionally, in-gel DNA footprinting with mutant substrates and modeling of an I-BmoI-substrate complex suggest that amino acid contacts to a critical GC-2 base pair are required to induce a bottom-strand distortion that likely directs conformational changes for reaction progress. Collectively, our data implies mechanistic roles for divalent metal ion and substrate bases, suggesting that divalent metal ion facilitates the re-positioning of the GIY-YIG nuclease domain between sequential nicking reactions.

Manipulative Properties of Asymmetric Double Quantum Dots via Laser and Gate Voltage

International Nuclear Information System (INIS)

Shun-Cai, Zhao; Zheng-Dong, Liu

2009-01-01

We present a density matrix approach for the theoretical description of an asymmetric double quantum dot (QD) system. The results show that the properties of gain, absorption and dispersion of the double QD system, the population of the state with one hole in one dot and an electron in another dot transferred by tunneling can be manipulated by a laser pulse or gate voltage. Our scheme may demonstrate the possibility of electro-optical manipulation of quantum systems. (condensed matter: electronicstructure, electrical, magnetic, and opticalproperties)

Asymmetric double Langmuir probe: Small signal application

International Nuclear Information System (INIS)

Uckan, T.

1987-11-01

We discuss the asymmetric double Langmuir probe (ADLP) and demonstrate the possibility of using it to measure plasma temperature T/sub e/ and density n when it is operated in the region of small signal response. The area of one of the ADLP collectors is considerably larger than the other. This probe can be operated at a relatively low applied voltage, eV/sub a/T/sub e/ < 1, and still provides sufficient information to determine the plasma T/sub e/ and n. There is no need for a direct measurement of the ion saturation current, which can be on the order of a few amperes in large fusion devices. This reduces the requirements on the probe power supply. 6 refs., 6 figs

Interference experiment with asymmetric double slit by using 1.2-MV field emission transmission electron microscope.

Science.gov (United States)

Harada, Ken; Akashi, Tetsuya; Niitsu, Kodai; Shimada, Keiko; Ono, Yoshimasa A; Shindo, Daisuke; Shinada, Hiroyuki; Mori, Shigeo

2018-01-17

Advanced electron microscopy technologies have made it possible to perform precise double-slit interference experiments. We used a 1.2-MV field emission electron microscope providing coherent electron waves and a direct detection camera system enabling single-electron detections at a sub-second exposure time. We developed a method to perform the interference experiment by using an asymmetric double-slit fabricated by a focused ion beam instrument and by operating the microscope under a "pre-Fraunhofer" condition, different from the Fraunhofer condition of conventional double-slit experiments. Here, pre-Fraunhofer condition means that each single-slit observation was performed under the Fraunhofer condition, while the double-slit observations were performed under the Fresnel condition. The interference experiments with each single slit and with the asymmetric double slit were carried out under two different electron dose conditions: high-dose for calculation of electron probability distribution and low-dose for each single electron distribution. Finally, we exemplified the distribution of single electrons by color-coding according to the above three types of experiments as a composite image.

Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.

Science.gov (United States)

Yahara, Koji; Fukuyo, Masaki; Sasaki, Akira; Kobayashi, Ichizo

2009-11-03

Homing endonuclease genes are "selfish" mobile genetic elements whose endonuclease promotes the spread of its own gene by creating a break at a specific target site and using the host machinery to repair the break by copying and inserting the gene at this site. Horizontal transfer across the boundary of a species or population within which mating takes place has been thought to be necessary for their evolutionary persistence. This is based on the assumption that they will become fixed in a host population, where opportunities of homing will disappear, and become susceptible to degeneration. To test this hypothesis, we modeled behavior of a homing endonuclease gene that moves during meiosis through double-strand break repair. We mathematically explored conditions for persistence of the homing endonuclease gene and elucidated their parameter dependence as phase diagrams. We found that, if the cost of the pseudogene is lower than that of the homing endonuclease gene, the 2 forms can persist in a population through autonomous periodic oscillation. If the cost of the pseudogene is higher, 2 types of dynamics appear that enable evolutionary persistence: bistability dependent on initial frequency or fixation irrespective of initial frequency. The prediction of long persistence in the absence of horizontal transfer was confirmed by stochastic simulations in finite populations. The average time to extinction of the endonuclease gene was found to be thousands of meiotic generations or more based on realistic parameter values. These results provide a solid theoretical basis for an understanding of these and other extremely selfish elements.

Improved image quality for asymmetric double-focal cone-beam SPECT

International Nuclear Information System (INIS)

Cao, Z.J.; Tsui, B.M.W.

1993-01-01

To optimize both spatial resolution and detection efficiency in brain SPECT imaging using a rectangular camera, an asymmetric double-focal cone-beam collimator is proposed with the focal points located near the base plane of the patient's head. To fit the entire head into the field-of-view of the collimator with dimensions of 50cmx40cm and at a radius-of-rotation of 15 cm, the focal lengths of the collimator are 55 and 70 cm, respectively, in the transverse and axial directions. With this geometry, the artifacts in the reconstructed image produced by the Feldkamp algorithm are more severe compared to those in a symmetric cone-beam geometry, due to the larger vertex angle between the top of the head and the base plane. To improve the reconstructed image quality, a fully three-dimensional (3D) reconstruction algorithm developed previously for single-focal cone-beam SPECT was extended to the asymmetric double-focal cone-beam geometry. The algorithm involves nonstationary 2D filtering and a reprojection technique for estimation of the missing data caused by a single-orbit cone-beam geometry. The results from simulation studies with the 3D Defrise slab phantom demonstrated that the fully 3D algorithm provided a much improved image quality in terms of reduced slice-to-slice cross talks and shape elongation compared to that produced by the conventional Feldkamp algorithm

Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea

OpenAIRE

Ishino, Sonoko; Nishi, Yuki; Oda, Soichiro; Uemori, Takashi; Sagara, Takehiro; Takatsu, Nariaki; Yamagami, Takeshi; Shirai, Tsuyoshi; Ishino, Yoshizumi

2016-01-01

The common mismatch repair system processed by MutS and MutL and their homologs was identified in Bacteria and Eukarya. However, no evidence of a functional MutS/L homolog has been reported for archaeal organisms, and it is not known whether the mismatch repair system is conserved in Archaea. Here, we describe an endonuclease that cleaves double-stranded DNA containing a mismatched base pair, from the hyperthermophilic archaeon Pyrococcus furiosus. The corresponding gene revealed that the act...

The Asymmetric Continental Shelf Wave in Response to the Synoptic Wind Burst in a Semienclosed Double-Shelf Basin

Science.gov (United States)

Qu, Lixin; Lin, Xiaopei; Hetland, Robert D.; Guo, Jingsong

2018-01-01

The primary goal of this study is to investigate the asymmetric structure of continental shelf wave in a semienclosed double-shelf basin, such as the Yellow Sea. Supported by in situ observations and realistic numerical simulations, it is found that in the Yellow Sea, the shelf wave response to the synoptic wind forcing does not match the mathematically symmetric solution of classic double-shelf wave theory, but rather exhibits a westward shift. To study the formation mechanism of this asymmetric structure, an idealized model was used and two sets of experiments were conducted. The results confirm that the asymmetric structure is due to the existence of a topographic waveguide connecting both shelves. For a semienclosed basin, such as the Yellow Sea, a connection at the end of the basin eliminates the potential vorticity barrier between the two shelves and hence plays a role as a connecting waveguide for shelf waves. This waveguide enables the shelf wave to propagate from one shelf to the other shelf and produces the asymmetric response in sea level and upwind flow evolutions.

Survival of Saccharomyces cerevisiae after treatment with the restriction endonuclease Alu I

International Nuclear Information System (INIS)

Winckler, K.; Bach, B.; Obe, G.

1988-01-01

Treatment of yeast cells proficient in the repair of radiation damage (Saccharomyces cervisiae) with the restriction endonuclease Alu I leads to a positive dose-effect relationship between inactivation level and enzyme concentration. The data suggest an uptake of the active restriction enzyme into the cells and a relationship between induction of DNA double-strand breaks and cell killing. (author)

Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4 and Micrococcus luteus uv-specific endonucleases

International Nuclear Information System (INIS)

Gordon, L.K.; Haseltine, W.A.

1980-01-01

A comparison was made of the activity of the uv-specific endonucleases of bacteriophage T4 (T4 endonuclease V) and of Micrococcus luteus on ultraviolet light-irradiated DNA substrates of defined sequence. The two enzyms cleave DNA at the site of pyrimidine dimers with the same frequency. The products of the cleavage reaction are the same. The pyrimidine dimer DNA-glycosylase activity of both enzymes is more active on double-stranded DNA than it is on single-stranded DNA

Type II restriction endonucleases : a historical perspective and more

OpenAIRE

Pingoud, Alfred; Wilson, Geoffrey G.; Wende, Wolfgang

2014-01-01

This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss ‘Type II’ REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nea...

Comparison of symmetric and asymmetric double quantum well extended-cavity diode lasers for broadband passive mode-locking at 780  nm.

Science.gov (United States)

Christopher, Heike; Kovalchuk, Evgeny V; Wenzel, Hans; Bugge, Frank; Weyers, Markus; Wicht, Andreas; Peters, Achim; Tränkle, Günther

2017-07-01

We present a compact, mode-locked diode laser system designed to emit a frequency comb in the wavelength range around 780 nm. We compare the mode-locking performance of symmetric and asymmetric double quantum well ridge-waveguide diode laser chips in an extended-cavity diode laser configuration. By reverse biasing a short section of the diode laser chip, passive mode-locking at 3.4 GHz is achieved. Employing an asymmetric double quantum well allows for generation of a mode-locked optical spectrum spanning more than 15 nm (full width at -20  dB) while the symmetric double quantum well device only provides a bandwidth of ∼2.7  nm (full width at -20  dB). Analysis of the RF noise characteristics of the pulse repetition rate shows an RF linewidth of about 7 kHz (full width at half-maximum) and of at most 530 Hz (full width at half-maximum) for the asymmetric and symmetric double quantum well devices, respectively. Investigation of the frequency noise power spectral density at the pulse repetition rate shows a white noise floor of approximately 2100  Hz 2 /Hz and of at most 170  Hz 2 /Hz for the diode laser employing the asymmetric and symmetric double quantum well structures, respectively. The pulse width is less than 10 ps for both devices.

[Restriction endonuclease digest - melting curve analysis: a new SNP genotyping and its application in traditional Chinese medicine authentication].

Science.gov (United States)

Jiang, Chao; Huang, Lu-Qi; Yuan, Yuan; Chen, Min; Hou, Jing-Yi; Wu, Zhi-Gang; Lin, Shu-Fang

2014-04-01

Single nucleotide polymorphisms (SNP) is an important molecular marker in traditional Chinese medicine research, and it is widely used in TCM authentication. The present study created a new genotyping method by combining restriction endonuclease digesting with melting curve analysis, which is a stable, rapid and easy doing SNP genotyping method. The new method analyzed SNP genotyping of two chloroplast SNP which was located in or out of the endonuclease recognition site, the results showed that when attaching a 14 bp GC-clamp (cggcgggagggcgg) to 5' end of the primer and selecting suited endonuclease to digest the amplification products, the melting curve of Lonicera japonica and Atractylodes macrocephala were all of double peaks and the adulterants Shan-yin-hua and A. lancea were of single peaks. The results indicated that the method had good stability and reproducibility for identifying authentic medicines from its adulterants. It is a potential SNP genotyping method and named restriction endonuclease digest - melting curve analysis.

Asymmetric double Langmuir probe for fast and automatic measurements of plasma temperature

International Nuclear Information System (INIS)

Uckan, T.

1987-11-01

We present a fast technique for determining the plasma electron temperature T/sub e/ automatically from the small signal application of the asymmetric double Langmuir probe when it is operated in the region where -1 < eV/sub a/T/sub e/ < 1. The method described here is based on simple time and rms averages of the probe current that results from a sinusoidally varying applied voltage V/sub a/. 4 refs., 2 figs

Endonuclease IV Is the major apurinic/apyrimidinic endonuclease in Mycobacterium tuberculosis and is important for protection against oxidative damage.

Directory of Open Access Journals (Sweden)

Rupangi Verma Puri

Full Text Available During the establishment of an infection, bacterial pathogens encounter oxidative stress resulting in the production of DNA lesions. Majority of these lesions are repaired by base excision repair (BER pathway. Amongst these, abasic sites are the most frequent lesions in DNA. Class II apurinic/apyrimidinic (AP endonucleases play a major role in BER of damaged DNA comprising of abasic sites. Mycobacterium tuberculosis, a deadly pathogen, resides in the human macrophages and is continually subjected to oxidative assaults. We have characterized for the first time two AP endonucleases namely Endonuclease IV (End and Exonuclease III (XthA that perform distinct functions in M.tuberculosis. We demonstrate that M.tuberculosis End is a typical AP endonuclease while XthA is predominantly a 3'→5' exonuclease. The AP endonuclease activity of End and XthA was stimulated by Mg(2+ and Ca(2+ and displayed a preferential recognition for abasic site paired opposite to a cytosine residue in DNA. Moreover, End exhibited metal ion independent 3'→5' exonuclease activity while in the case of XthA this activity was metal ion dependent. We demonstrate that End is not only a more efficient AP endonuclease than XthA but it also represents the major AP endonuclease activity in M.tuberculosis and plays a crucial role in defense against oxidative stress.

Influence of asymmetric magnetic perturbation on the nonlinear evolution of double tearing modes

Science.gov (United States)

Xiong, G. Z.; Wang, L.; Li, X. Q.; Liu, H. F.; Tang, C. J.; Huang, J.; Zhang, X.; Wang, X. Q.

2017-06-01

The effects of asymmetric magnetic perturbation on the triggering and evolution of double tearing modes (DTMs) are investigated using nonlinear magnetohydrodynamics simulations in a slab geometry. We find that for reversed magnetic shear plasmas the resistive reconnection process induced by the initial perturbation at one rational surface can drive a new island at the other rational surface with the same mode number. The four typical states of the mode for the time evolution are found, and include: (i) a linear growth stage; (ii) a linear/nonlinear stable stage; (iii) an interactively driving stage; and (iv) a symmetric DTM stage. These differ from previous simulation results. Moreover, nonlinear DTM growth is found to strongly depend on the asymmetric magnetic perturbation, particularly in the early nonlinear phase. The initial perturbation strength scale of island width suggests that the left island enters into a Sweet-Parker growth process when the right island is sufficiently large to effectively drive the other. These results predict that although externally applied magnetic perturbations can suppress the neoclassical tearing mode they can also trigger new instabilities such as asymmetric DTMs.

Influence of asymmetric magnetic perturbation on the nonlinear evolution of double tearing modes

International Nuclear Information System (INIS)

Xiong, G Z; Liu, H F; Huang, J; Wang, X Q; Wang, L; Li, X Q; Tang, C J; Zhang, X

2017-01-01

The effects of asymmetric magnetic perturbation on the triggering and evolution of double tearing modes (DTMs) are investigated using nonlinear magnetohydrodynamics simulations in a slab geometry. We find that for reversed magnetic shear plasmas the resistive reconnection process induced by the initial perturbation at one rational surface can drive a new island at the other rational surface with the same mode number. The four typical states of the mode for the time evolution are found, and include: (i) a linear growth stage; (ii) a linear/nonlinear stable stage; (iii) an interactively driving stage; and (iv) a symmetric DTM stage. These differ from previous simulation results. Moreover, nonlinear DTM growth is found to strongly depend on the asymmetric magnetic perturbation, particularly in the early nonlinear phase. The initial perturbation strength scale of island width suggests that the left island enters into a Sweet–Parker growth process when the right island is sufficiently large to effectively drive the other. These results predict that although externally applied magnetic perturbations can suppress the neoclassical tearing mode they can also trigger new instabilities such as asymmetric DTMs. (paper)

Karyopherin-mediated nuclear import of the homing endonuclease VMA1-derived endonuclease is required for self-propagation of the coding region.

Science.gov (United States)

Nagai, Yuri; Nogami, Satoru; Kumagai-Sano, Fumi; Ohya, Yoshikazu

2003-03-01

VMA1-derived endonuclease (VDE), a site-specific endonuclease in Saccharomyces cerevisiae, enters the nucleus to generate a double-strand break in the VDE-negative allelic locus, mediating the self-propagating gene conversion called homing. Although VDE is excluded from the nucleus in mitotic cells, it relocalizes at premeiosis, becoming localized in both the nucleus and the cytoplasm in meiosis. The nuclear localization of VDE is induced by inactivation of TOR kinases, which constitute central regulators of cell differentiation in S. cerevisiae, and by nutrient depletion. A functional genomic approach revealed that at least two karyopherins, Srp1p and Kap142p, are required for the nuclear localization pattern. Genetic and physical interactions between Srp1p and VDE imply direct involvement of karyopherin-mediated nuclear transport in this process. Inactivation of TOR signaling or acquisition of an extra nuclear localization signal in the VDE coding region leads to artificial nuclear localization of VDE and thereby induces homing even during mitosis. These results serve as evidence that VDE utilizes the host systems of nutrient signal transduction and nucleocytoplasmic transport to ensure the propagation of its coding region.

Yeast redoxyendonuclease, a DNA repair enzyme similar to Escherichia coli endonuclease III

International Nuclear Information System (INIS)

Gossett, J.; Lee, K.; Cunningham, R.P.; Doetsch, P.W.

1988-01-01

A DNA repair endonuclease (redoxyendonuclease) was isolated from bakers' yeast (Saccharomyces cerevisiae). The enzyme has been purified by a series of column chromatography steps and cleaves OsO 4 -damaged, double-stranded DNA at sites of thymine glycol and heavily UV-irradiated DNA at sites of cytosine, thymine, and guanine photoproducts. The base specificity and mechanism of phosphodiester bond cleavage for the yeast redoxyendonuclease appear to be identical with those of Escherichia coli endonuclease III when thymine glycol containing, end-labeled DNA fragments of defined sequence are employed as substrates. Yeast redoxyendonuclease has an apparent molecular size of 38,000-42,000 daltons and is active in the absence of divalent metal cations. The identification of such an enzyme in yeast may be of value in the elucidation of the biochemical basis for radiation sensitivity in certain yeast mutants

High Quality Plasmonic Sensors Based on Fano Resonances Created through Cascading Double Asymmetric Cavities.

Science.gov (United States)

Zhang, Xiangao; Shao, Mingzhen; Zeng, Xiaoqi

2016-10-18

In this paper, a type of compact nanosensor based on a metal-insulator-metal structure is proposed and investigated through cascading double asymmetric cavities, in which their metal cores shift along different axis directions. The cascaded asymmetric structure exhibits high transmission and sharp Fano resonance peaks via strengthening the mutual coupling of the cavities. The research results show that with the increase of the symmetry breaking in the structure, the number of Fano resonances increase accordingly. Furthermore, by modulating the geometrical parameters appropriately, Fano resonances with high sensitivities to the changes in refractive index can be realized. A maximum figure of merit (FoM) value of 74.3 is obtained. Considerable applications for this work can be found in bio/chemical sensors with excellent performance and other nanophotonic integrated circuit devices such as optical filters, switches and modulators.

Exploring the Short-Channel Characteristics of Asymmetric Junctionless Double-Gate Silicon-on-Nothing MOSFET

Science.gov (United States)

Saha, Priyanka; Banerjee, Pritha; Dash, Dinesh Kumar; Sarkar, Subir Kumar

2018-03-01

This paper presents an analytical model of an asymmetric junctionless double-gate (asymmetric DGJL) silicon-on-nothing metal-oxide-semiconductor field-effect transistor (MOSFET). Solving the 2-D Poisson's equation, the expressions for center potential and threshold voltage are calculated. In addition, the response of the device toward the various short-channel effects like hot carrier effect, drain-induced barrier lowering and threshold voltage roll-off has also been examined along with subthreshold swing and drain current characteristics. Performance analysis of the present model is also demonstrated by comparing its short-channel behavior with conventional DGJL MOSFET. The effect of variation of the device features due to the variation of device parameters is also studied. The simulated results obtained using 2D device simulator, namely ATLAS, are in good agreement with the analytical results, hence validating our derived model.

High Quality Plasmonic Sensors Based on Fano Resonances Created through Cascading Double Asymmetric Cavities

Directory of Open Access Journals (Sweden)

Xiangao Zhang

2016-10-01

Full Text Available In this paper, a type of compact nanosensor based on a metal-insulator-metal structure is proposed and investigated through cascading double asymmetric cavities, in which their metal cores shift along different axis directions. The cascaded asymmetric structure exhibits high transmission and sharp Fano resonance peaks via strengthening the mutual coupling of the cavities. The research results show that with the increase of the symmetry breaking in the structure, the number of Fano resonances increase accordingly. Furthermore, by modulating the geometrical parameters appropriately, Fano resonances with high sensitivities to the changes in refractive index can be realized. A maximum figure of merit (FoM value of 74.3 is obtained. Considerable applications for this work can be found in bio/chemical sensors with excellent performance and other nanophotonic integrated circuit devices such as optical filters, switches and modulators.

Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein.

Science.gov (United States)

Nam, Ki Hyun; Ding, Fran; Haitjema, Charles; Huang, Qingqiu; DeLisa, Matthew P; Ke, Ailong

2012-10-19

The CRISPR (clustered regularly interspaced short palindromic repeats) system is a prokaryotic RNA-based adaptive immune system against extrachromosomal genetic elements. Cas2 is a universally conserved core CRISPR-associated protein required for the acquisition of new spacers for CRISPR adaptation. It was previously characterized as an endoribonuclease with preference for single-stranded (ss)RNA. Here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the Bacillus halodurans Cas2 (Bha_Cas2) from the subtype I-C/Dvulg CRISPR instead possesses metal-dependent endonuclease activity against double-stranded (ds)DNA. This activity is consistent with its putative function in producing new spacers for insertion into the 5'-end of the CRISPR locus. Mutagenesis and isothermal titration calorimetry studies revealed that a single divalent metal ion (Mg(2+) or Mn(2+)), coordinated by a symmetric Asp pair in the Bha_Cas2 dimer, is involved in the catalysis. We envision that a pH-dependent conformational change switches Cas2 into a metal-binding competent conformation for catalysis. We further propose that the distinct substrate preferences among Cas2 proteins may be determined by the sequence and structure in the β1-α1 loop.

Endonuclease activities in extracts of Micrococcus luteus that act on. gamma. -irradiated DNA

Energy Technology Data Exchange (ETDEWEB)

Schoen-Bopp, A; Schaefer, G; Hagen, U [Kernforschungszentrum Karlsruhe (Germany, F.R.). Inst. fuer Strahlenbiologie

1977-03-01

Several protein fractions containing endonuclease activity against ..gamma..-irradiated DNA (..gamma..-endonuclease) were isolated from M.luteus. The crude extract was eluted on a phosphocellulose column and chromatographed on TEAE cellulose and subsequently on hydroxypatite. Five peaks of ..gamma..-endonuclease were obtained from each preparation. Repeated experiments showed comparable chromatographic behaviour of the fractions. There was no detectable activity of uv-endonuclease in the fractions with ..gamma..-endonuclease but a small contamination of endonuclease against unirradiated DNA and against DNA with apurinic sites. The ..gamma..-endonuclease was stimulated by, but was not dependent on, magnesium. Several tests for endonuclease activity have been used: the analysis of strand breaks in calf-thymus DNA or in PM2 DNA, and the determination of end-groups formed by endonuclease, either 3'OH end-groups or phosphomonoester end groups. From the results obtained it can be assumed that the strand breaks induced by the ..gamma..-endonuclease carry 3'OH and 5' phosphate end groups.

Tunnel magnetoresistance in asymmetric double-barrier magnetic tunnel junctions

International Nuclear Information System (INIS)

Useinov, N.Kh.; Petukhov, D.A.; Tagirov, L.R.

2015-01-01

The spin-polarized tunnel conductance and tunnel magnetoresistance (TMR) through a planar asymmetric double-barrier magnetic tunnel junction (DBMTJ) have been calculated using quasi-classical model. In DBMTJ nanostructure the magnetization of middle ferromagnetic metal layer can be aligned parallel or antiparallel with respect to the fixed magnetizations of the top and bottom ferromagnetic electrodes. The transmission coefficients of an electron to pass through the barriers have been calculated in terms of quantum mechanics. The dependencies of tunnel conductance and TMR on the applied voltage have been calculated in case of non-resonant transmission. Estimated in the framework of our model, the difference between the spin-channels conductances at low voltages was found relatively large. This gives rise to very high magnitude of TMR. - Highlights: • The spin-polarized conductance through the junction is calculated. • Dependencies of the tunnel conductance vs applied bias are shown. • Bias voltage dependence of tunnel magnetoresistance for the structure is shown

Controllable optical bistability and multistability in asymmetric double quantum wells via spontaneously generated coherence

Energy Technology Data Exchange (ETDEWEB)

Chen, Yuan; Deng, Li [Department of Applied Physics, East China Jiaotong University, Nanchang, 330013 (China); Chen, Aixi, E-mail: aixichen@ecjtu.jx.cn [Department of Applied Physics, East China Jiaotong University, Nanchang, 330013 (China); Institute for Quantum Computing, University of Waterloo, Ontario N2L 3G1 (Canada)

2015-02-15

We investigate the nonlinear optical phenomena of the optical bistability and multistability via spontaneously generated coherence in an asymmetric double quantum well structure coupled by a weak probe field and a controlling field. It is shown that the threshold and hysteresis cycle of the optical bistability can be conveniently controlled only by adjusting the intensity of the SGC or the controlling field. Moreover, switching between optical bistability and multistability can be achieved. These studies may have practical significance for the preparation of optical bistable switching device.

Controllable optical bistability and multistability in asymmetric double quantum wells via spontaneously generated coherence

International Nuclear Information System (INIS)

Chen, Yuan; Deng, Li; Chen, Aixi

2015-01-01

We investigate the nonlinear optical phenomena of the optical bistability and multistability via spontaneously generated coherence in an asymmetric double quantum well structure coupled by a weak probe field and a controlling field. It is shown that the threshold and hysteresis cycle of the optical bistability can be conveniently controlled only by adjusting the intensity of the SGC or the controlling field. Moreover, switching between optical bistability and multistability can be achieved. These studies may have practical significance for the preparation of optical bistable switching device

Spectroelectrochemical insights into structural and redox properties of immobilized endonuclease III and its catalytically inactive mutant

Science.gov (United States)

Moe, Elin; Rollo, Filipe; Silveira, Célia M.; Sezer, Murat; Hildebrandt, Peter; Todorovic, Smilja

2018-01-01

Endonuclease III is a Fe-S containing bifunctional DNA glycosylase which is involved in the repair of oxidation damaged DNA. Here we employ surface enhanced IR spectroelectrochemistry and electrochemistry to study the enzyme from the highly radiation- and desiccation-resistant bacterium Deinococcus radiodurans (DrEndoIII2). The experiments are designed to shed more light onto specific parameters that are currently proposed to govern damage search and recognition by endonucleases III. We demonstrate that electrostatic interactions required for the redox activation of DrEndoIII2 may result in high electric fields that alter its structural and thermodynamic properties. Analysis of inactive DrEndoIII2 (K132A/D150A double mutant) interacting with undamaged DNA, and the active enzyme interacting with damaged DNA also indicate that the electron transfer is modulated by subtle differences in the protein-DNA complex.

Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis.

Science.gov (United States)

Zhang, Wei; Xu, Yueyang; Yan, Mengrong; Li, Shanshan; Wang, Huiying; Yang, Haitao; Zhou, Weihong; Rao, Zihe

2018-03-25

Endonuclease IV is a typical endonuclease of the apurinic-apyrimidinic (AP) or abasic endonuclease superfamily. It repairs damaged DNA through base excision repair by cleaving the DNA backbone immediately 5' of an AP site. In Mycobacterium tuberculosis, endonuclease IV is the major AP endonuclease. This enzyme is absent from mammalian cells, making it an attractive target for anti-tuberculosis drug development. In this study, the structure of the recombinant endonuclease IV from M. tuberculosis (MtbEndo IV) was determined at a high resolution of 1.18 Å. MtbEndo IV was found to have a classical α8β8-fold TIM barrel with loops on its surface connecting the α-helices and β-strands that constitute a groove for DNA binding. Three zinc ions were identified at the active site. A comparison between the structures of MtbEndo IV and Escherichia coli End IV suggested that Gln32 of MtbEndo IV may plays a role in regulating substrate binding. Copyright © 2018. Published by Elsevier Inc.

Electrical Double-Layer and Ion Bridging Forces between Symmetric and Asymmetric Charged Surfaces in the Presence of Mono- and Divalent Ions

DEFF Research Database (Denmark)

Liu, Xiaoyan; Feilberg, Karen Louise; Yan, Wei

2017-01-01

charged (3-aminopropyl)trimethoxysilane, and the negatively charged (3-mercaptopropyl)trimethoxysilane. The interactions between the three symmetric systems, as well as between the three asymmetric combinations of surfaces, were measured and compared to calculated electrical double-layer forces...

Endonuclease IV of Escherichia coli is induced by paraquat

Energy Technology Data Exchange (ETDEWEB)

Chan, E.; Weiss, B.

1987-05-01

The addition of paraquat (methyl viologen) to a growing culture of Escherichia coli K-12 led within 1 hr to a 10- to 20-fold increase in the level of endonuclease IV, a DNase for apurinic/apyrimidinic sites. The induction was blocked by chloramphenicol. Increases of 3-fold or more were also seen with plumbagin, menadione, and phenazine methosulfate. H/sub 2/O/sub 2/ produced no more than a 2-fold increase in endonuclease IV activity. The following agents had no significant effect: streptonigrin, nitrofurantoin, tert-butyl hydroperoxide, ..gamma.. rays, 260-nm UV radiation, methyl methanesulfonate, mitomycin C, and ascorbate. Paraquat, plumbagin, menadione, and phenazine methosulfate are known to generate superoxide radical anions via redox cycling in vivo. A mutant lacking superoxide dismutase was unusually sensitive to induction by paraquat. In addition, endonuclease IV could be induced by merely growing the mutant in pure O/sub 2/. The levels of endonuclease IV in uninduced or paraquat-treated cells were unaffected by mutations of oxyR, a H/sub 2/O/sub 2/-inducible gene that governs an oxidative-stress regulon. The results indicate that endonuclease IV is an inducible DNA-repair enzyme and that its induction can be mediated via the production of superoxide radicals.

Endonuclease IV of Escherichia coli is induced by paraquat

International Nuclear Information System (INIS)

Chan, E.; Weiss, B.

1987-01-01

The addition of paraquat (methyl viologen) to a growing culture of Escherichia coli K-12 led within 1 hr to a 10- to 20-fold increase in the level of endonuclease IV, a DNase for apurinic/apyrimidinic sites. The induction was blocked by chloramphenicol. Increases of 3-fold or more were also seen with plumbagin, menadione, and phenazine methosulfate. H 2 O 2 produced no more than a 2-fold increase in endonuclease IV activity. The following agents had no significant effect: streptonigrin, nitrofurantoin, tert-butyl hydroperoxide, γ rays, 260-nm UV radiation, methyl methanesulfonate, mitomycin C, and ascorbate. Paraquat, plumbagin, menadione, and phenazine methosulfate are known to generate superoxide radical anions via redox cycling in vivo. A mutant lacking superoxide dismutase was unusually sensitive to induction by paraquat. In addition, endonuclease IV could be induced by merely growing the mutant in pure O 2 . The levels of endonuclease IV in uninduced or paraquat-treated cells were unaffected by mutations of oxyR, a H 2 O 2 -inducible gene that governs an oxidative-stress regulon. The results indicate that endonuclease IV is an inducible DNA-repair enzyme and that its induction can be mediated via the production of superoxide radicals

Endonucleases induced TRAIL-insensitive apoptosis in ovarian carcinoma cells

Energy Technology Data Exchange (ETDEWEB)

Geel, Tessa M. [Department of Pathology and Medical Biology, Groningen University Institute for Drug Exploration (GUIDE), University Medical Center Groningen (UMCG), Hanzeplein 1, 9713 GZ, Groningen (Netherlands); Meiss, Gregor [Institute of Biochemistry, Justus-Liebig-University Giessen, D-35392 Giessen (Germany); Gun, Bernardina T. van der; Kroesen, Bart Jan; Leij, Lou F. de [Department of Pathology and Medical Biology, Groningen University Institute for Drug Exploration (GUIDE), University Medical Center Groningen (UMCG), Hanzeplein 1, 9713 GZ, Groningen (Netherlands); Zaremba, Mindaugas; Silanskas, Arunas [Institute of Biotechnology, Vilnius LT-02241 (Lithuania); Kokkinidis, Michael [IMBB/FORTH and University of Crete/Department of Biology, GR-71409 Heraklion/Crete (Greece); Pingoud, Alfred [Institute of Biochemistry, Justus-Liebig-University Giessen, D-35392 Giessen (Germany); Ruiters, Marcel H. [Department of Pathology and Medical Biology, Groningen University Institute for Drug Exploration (GUIDE), University Medical Center Groningen (UMCG), Hanzeplein 1, 9713 GZ, Groningen (Netherlands); Synvolux therapeutics, Groningen (Netherlands); McLaughlin, Pamela M. [Department of Pathology and Medical Biology, Groningen University Institute for Drug Exploration (GUIDE), University Medical Center Groningen (UMCG), Hanzeplein 1, 9713 GZ, Groningen (Netherlands); Rots, Marianne G., E-mail: m.g.rots@med.umcg.nl [Department of Pathology and Medical Biology, Groningen University Institute for Drug Exploration (GUIDE), University Medical Center Groningen (UMCG), Hanzeplein 1, 9713 GZ, Groningen (Netherlands)

2009-09-10

TRAIL induced apoptosis of tumor cells is currently entering phase II clinical settings, despite the fact that not all tumor types are sensitive to TRAIL. TRAIL resistance in ovarian carcinomas can be caused by a blockade upstream of the caspase 3 signaling cascade. We explored the ability of restriction endonucleases to directly digest DNA in vivo, thereby circumventing the caspase cascade. For this purpose, we delivered enzymatically active endonucleases via the cationic amphiphilic lipid SAINT-18{sup Registered-Sign }:DOPE to both TRAIL-sensitive and insensitive ovarian carcinoma cells (OVCAR and SKOV-3, respectively). Functional nuclear localization after delivery of various endonucleases (BfiI, PvuII and NucA) was indicated by confocal microscopy and genomic cleavage analysis. For PvuII, analysis of mitochondrial damage demonstrated extensive apoptosis both in SKOV-3 and OVCAR. This study clearly demonstrates that cellular delivery of restriction endonucleases holds promise to serve as a novel therapeutic tool for the treatment of resistant ovarian carcinomas.

Why Public Employment Services Always Fail. Double-sided Asymmetric Information and the Replacement of Low-skill Workers in six European Countries

DEFF Research Database (Denmark)

Larsen, Christian Albrekt; Vesan, Patrik

2012-01-01

It has been a general finding across Europe that very few job matches are facilitated by public employment services (PES).The article explains this failure by highlighting the existence of a double-sided asymmetric information problem on the labour market. It is argued that although a PES...

Endonuclease α from Saccharomyces cerevisiae shows increased activity on ultraviolet irradiated native DNA

International Nuclear Information System (INIS)

Bryant, D.W.; Haynes, R.H.

1978-01-01

Endonuclease α isolated from the nucleus of the yeast Saccharomyces cerevisiae is a DNA endonuclease which has been shown to act preferentially on denatured T7 DNA. The purified enzyme is more active with UV-irradiated native T7 DNA than with unirradiated substrate. The relation between damage, measured by pyrimidine dimer concentration, and excess endonuclease activity is most readily explained by local denaturation caused by the presence of pyrimidine dimers. When three radiation sensitive mutants of yeast were tested for the level of endonuclease α present, none were found lacking the enzyme. However, nuclei of strain rad 1-1, a mutant that may be defective in heteroduplex repair as well as excision repair, were found to contain reduced levels of the endonuclease. (orig./AJ) [de

Four-wave mixing in an asymmetric double quantum dot molecule

Science.gov (United States)

Kosionis, Spyridon G.

2018-06-01

The four-wave mixing (FWM) effect of a weak probe field, in an asymmetric semiconductor double quantum dot (QD) structure driven by a strong pump field is theoretically studied. Similarly to the case of examining several other nonlinear optical processes, the nonlinear differential equations of the density matrix elements are used, under the rotating wave approximation. By suitably tuning the intensity and the frequency of the pump field as well as by changing the value of the applied bias voltage, a procedure used to properly adjust the electron tunneling coupling, we control the FWM in the same way as several other nonlinear optical processes of the system. While in the weak electron tunneling regime, the impact of the pump field intensity on the FWM is proven to be of crucial importance, for even higher rates of the electron tunneling it is evident that the intensity of the pump field has only a slight impact on the form of the FWM spectrum. The number of the spectral peaks, depends on the relation between specific parameters of the system.

Transient gain property of a weak probe field in an asymmetric semiconductor coupled double quantum well structure

International Nuclear Information System (INIS)

Wang Zhigang; Zheng Zhiren; Yu Junhua

2007-01-01

The transient gain property of a weak probe field in an asymmetric semiconductor coupled double quantum well structure is reported. The transient process of the system, which is induced by the external coherent coupling field, shows the property of no inverse gain. We find that the transient behavior of the probe field can be tuned by the change of tunneling barrier. Both the amplitude of the transient gain and the frequency of the oscillation can be affected by the lifetime broadening

Chaos of several typical asymmetric systems

International Nuclear Information System (INIS)

Feng Jingjing; Zhang Qichang; Wang Wei

2012-01-01

The threshold for the onset of chaos in asymmetric nonlinear dynamic systems can be determined using an extended Padé method. In this paper, a double-well asymmetric potential system with damping under external periodic excitation is investigated, as well as an asymmetric triple-well potential system under external and parametric excitation. The integrals of Melnikov functions are established to demonstrate that the motion is chaotic. Threshold values are acquired when homoclinic and heteroclinic bifurcations occur. The results of analytical and numerical integration are compared to verify the effectiveness and feasibility of the analytical method.

Asymmetric voltage behavior of the tunnel magnetoresistance in double barrier magnetic tunnel junctions

KAUST Repository

Useinov, Arthur

2012-06-01

In this paper, we study the value of the tunnel magnetoresistance (TMR) as a function of the applied voltage in double barrier magnetic tunnel junctions (DMTJs) with the left and right ferromagnetic (FM) layers being pinned and numerically estimate the possible difference of the TMR curves for negative and positive voltages in the homojunctions (equal barriers and electrodes). DMTJs are modeled as two single barrier junctions connected in series with consecutive tunneling (CST). We investigated the asymmetric voltage behavior of the TMR for the CST in the range of a general theoretical model. Significant asymmetries of the experimental curves, which arise due to different annealing regimes, are mostly explained by different heights of the tunnel barriers and asymmetries of spin polarizations in magnetic layers. © (2012) Trans Tech Publications.

Asymmetric voltage behavior of the tunnel magnetoresistance in double barrier magnetic tunnel junctions

KAUST Repository

Useinov, Arthur; Gooneratne, Chinthaka Pasan; Kosel, Jü rgen

2012-01-01

In this paper, we study the value of the tunnel magnetoresistance (TMR) as a function of the applied voltage in double barrier magnetic tunnel junctions (DMTJs) with the left and right ferromagnetic (FM) layers being pinned and numerically estimate the possible difference of the TMR curves for negative and positive voltages in the homojunctions (equal barriers and electrodes). DMTJs are modeled as two single barrier junctions connected in series with consecutive tunneling (CST). We investigated the asymmetric voltage behavior of the TMR for the CST in the range of a general theoretical model. Significant asymmetries of the experimental curves, which arise due to different annealing regimes, are mostly explained by different heights of the tunnel barriers and asymmetries of spin polarizations in magnetic layers. © (2012) Trans Tech Publications.

Induction of DNA double-strand breaks by restriction enzymes in X-ray-sensitive mutant Chinese hamster ovary cells measured by pulsed-field gel electrophoresis

International Nuclear Information System (INIS)

Kinashi, Yuko; Nagasawa, Hatsumi; Little, J.B.; Okayasu, Ryuichi; Iliakis, G.E.

1995-01-01

This investigation was designed to determine whether the cytotoxic effects of different restriction endonucleases are related to the number and type of DNA double-strand breaks (DSBs) they produce. Chinese hamster ovary (CHO) K1 and xrs-5 cells, a radiosensitive mutant of CHO K1, were exposed to restriction endonucleases HaeIII, HinfI, PvuII and BamHI by electroporation. These enzymes represent both blunt and sticky end cutters with differing recognition sequence lengths. The number of DSBs was measured by pulsed-field gel electrophoresis (PFGE). Two forms of PFGE were employed: asymmetric field-inversion gel electrophoresis (AFIGE) for measuring the kinetics of DNA breaks by enzyme digestion and clamped homogeneous gel electrophoresis (CHEF) for examining the size distributions of damaged DNA. The amount of DNA damage induced by exposure to all four restriction enzymes was significantly greater in xrs-5 compared to CHO K1 cells, consistent with the reported DSB repair deficiency in these cells. Since restriction endonucleases produce DSBs alone as opposed to the various types of DNA damage induced by X rays, these results confirm that the repair defect in this mutant involves the rejoining of DSBs. Although the cutting frequency was directly related to the length of the recognition sequence for four restriction enzymes, there was no simple correlation between the cytotoxic effect and the amount of DNA damage produced by each enzyme in either cell line. This finding suggests that the type or nature of the cutting sequence itself may play a role in restriction enzyme-induced cell killing. 32 refs., 6 figs., 3 tabs

Identification of flap structure-specific endonuclease 1 as a factor involved in long-term memory formation of aversive learning.

Science.gov (United States)

Saavedra-Rodríguez, Lorena; Vázquez, Adrinel; Ortiz-Zuazaga, Humberto G; Chorna, Nataliya E; González, Fernando A; Andrés, Lissette; Rodríguez, Karen; Ramírez, Fernando; Rodríguez, Alan; Peña de Ortiz, Sandra

2009-05-06

We previously proposed that DNA recombination/repair processes play a role in memory formation. Here, we examined the possible role of the fen-1 gene, encoding a flap structure-specific endonuclease, in memory consolidation of conditioned taste aversion (CTA). Quantitative real-time PCR showed that amygdalar fen-1 mRNA induction was associated to the central processing of the illness experience related to CTA and to CTA itself, but not to the central processing resulting from the presentation of a novel flavor. CTA also increased expression of the Fen-1 protein in the amygdala, but not the insular cortex. In addition, double immunofluorescence analyses showed that amygdalar Fen-1 expression is mostly localized within neurons. Importantly, functional studies demonstrated that amygdalar antisense knockdown of fen-1 expression impaired consolidation, but not short-term memory, of CTA. Overall, these studies define the fen-1 endonuclease as a new DNA recombination/repair factor involved in the formation of long-term memories.

Molecular mechanisms involved in the production of chromosomal aberrations. I. Utilization of Neurospora endonuclease for the study of aberration production in G2 stage of the cell cycle

Energy Technology Data Exchange (ETDEWEB)

Natarajan, A T; Obe, G [Rijksuniversiteit Leiden (Netherlands). J.A. Cohen Inst. voor Radiopathologie en Stralingsbescherming

1978-10-01

Chinese hamster ovary cells (CHO) were X-irradiated in G2 stage of the cell cycle and immediately treated, in the presence of inactivated Sendai virus, with Neurospora endonuclease (E.C. 3.1.4.), an enzyme which is specific for cleaving single-stranded DNA. With this treatment, the frequencies of all types of chromosome aberrations increased when compared to X-irradiated controls. These results are interpreted as due to the conversion of some of the X-ray induced single-stranded DNA breaks into double-strand breaks by this enzyme. Similar enhancement due to this enzyme was found following treatment with methyl methanesulfonate (MMS) and bleomycin, but not following UV and mitomycin C. Addition of Micrococcus endonuclease and Neurospora endonuclease to the cells did not alter the frequencies of aberrations induced by UV. The introduction of enzymes with specific DNA-repair function offers possibilities to probe into the molecular events involved in the formation of structural chromosome aberrations induced by different classes of physical and chemical mutagens.

Binding of T4 endonuclease V to deoxyribonucleic acid irradiated with ultraviolet light

International Nuclear Information System (INIS)

Seawell, P.C.; Simon, T.J.; Ganesan, A.K.

1980-01-01

Endonuclease V of bacteriophage T4 binds to uv-irradiated deoxyribonucleic acid (DNA) but not to unirradiated DNA. We have developed an assay to detect this binding, based on the retention of enzyme - DNA complexes on nitrocellulose filters. The amount of complex retained, ascertained by using radioactive DNA, is a measure of T4 endonuclease V activity. From our data we conclude that (1) T4 endonuclease V binds to uv-irradiated DNA but not to DNA that has been previously incised by the endonuclease, (2) equilibrium between the free and complexed form of the enzyme is attained under our reaction conditions, (3) dissociation of enzyme - DNA complexes is retarded by sodium cyanide, and (4) retention of enzyme - DNA complexes on nitrocellulose filters is enhanced by high concentrations of saline-citrate

The Dissolution of Double Holliday Junctions

DEFF Research Database (Denmark)

Bizard, Anna H; Hickson, Ian D

2014-01-01

as "double Holliday junction dissolution." This reaction requires the cooperative action of a so-called "dissolvasome" comprising a Holliday junction branch migration enzyme (Sgs1/BLM RecQ helicase) and a type IA topoisomerase (Top3/TopoIIIα) in complex with its OB (oligonucleotide/oligosaccharide binding......Double Holliday junctions (dHJS) are important intermediates of homologous recombination. The separate junctions can each be cleaved by DNA structure-selective endonucleases known as Holliday junction resolvases. Alternatively, double Holliday junctions can be processed by a reaction known......) fold containing accessory factor (Rmi1). This review details our current knowledge of the dissolution process and the players involved in catalyzing this mechanistically complex means of completing homologous recombination reactions....

Hierarchical Ni-Co layered double hydroxide nanosheets on functionalized 3D-RGO films for high energy density asymmetric supercapacitor

Science.gov (United States)

Jiang, Liyang; Sui, Yanwei; Qi, Jiqiu; Chang, Yuan; He, Yezeng; Meng, Qingkun; Wei, Fuxiang; Sun, Zhi; Jin, Yunxue

2017-12-01

In this paper, ultrathin reduced graphene oxide films on nickel foam were fabricated via a facile dip-coating method combined with thermal reduction. Hierarchical Ni-Co layered double hydroxide nanosheets with network structure were electrodeposited on the ultrathin reduced graphene oxide films in a simple three-electrode system. The thickness of Ni-Co layered double hydroxide nanosheets can be controlled through adjusting the deposition temperature. The as-prepared electrode exhibited excellent electrochemical performance with specific capacitance of 1454.2 F g-1 at a current density of 1 A g-1. An asymmetric supercapacitor device was designed with the as-prepared composites as positive electrode material and Nitrogen-doped reduced graphene oxide as negative electrode material. This device could be operated in a working voltage range of 0-1.8 V in 1 M KOH aqueous electrolyte, delivering a high energy density of 56.4 W h kg-1 at a power density of 882.5 W kg-1. One supercapacitor can power two LEDs with rated voltage of 1.8-2.0 V. After 10,000 consecutive charge-discharge tests at 10 A g-1, this asymmetric supercapacitor revealed an excellent cycle life with 98.3% specific capacitance retention. These excellent electrochemical performances make it become one of most promising candidates for high energy supercapacitor device.

Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA.

Directory of Open Access Journals (Sweden)

Guang Liu

2010-12-01

Full Text Available Many taxonomically diverse prokaryotes enzymatically modify their DNA by replacing a non-bridging oxygen with a sulfur atom at specific sequences. The biological implications of this DNA S-modification (phosphorothioation were unknown. We observed that simultaneous expression of the dndA-E gene cluster from Streptomyces lividans 66, which is responsible for the DNA S-modification, and the putative Streptomyces coelicolor A(32 Type IV methyl-dependent restriction endonuclease ScoA3McrA (Sco4631 leads to cell death in the same host. A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links. DNase I footprinting demonstrated binding of ScoA3McrA to the Dcm methylation site, but no clear binding could be detected at the S-modified site under cleavage conditions. This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA.

Simple and sensitive fluorescence assay of restriction endonuclease on graphene oxide

International Nuclear Information System (INIS)

Gang, Jong Back

2015-01-01

Restriction endonucleases hydrolyze internal phosphodiester bonds at specific sites in a DNA sequence. These enzymes are essential in a variety of fields, such as biotechnology and clinical diagnostics. It is of great importance and necessity for the scientific and biomedical use of enzymes to measure endonuclease activity. In this study, graphene oxide (GO) has been used as a platform to measure enzyme activity with high sensitivity. To increase the detection sensitivity of Hinf I, the endonuclease-digested reaction was treated with exonuclease III (Exo III) and a fluorescence assay was conducted to measure the emission. Results showed that Exo III treatment enhanced 2.7-fold signal-to-background ratio for the detection of Hinf I compared with that done without Exo III in the presence of GO

The Helicobacter pylori HpyAXII restriction–modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components

Science.gov (United States)

Humbert, Olivier; Salama, Nina R.

2008-01-01

The naturally competent organism Helicobacter pylori encodes a large number of restriction–modification (R–M) systems that consist of a restriction endonuclease and a DNA methyltransferase. R–M systems are not only believed to limit DNA exchange among bacteria but may also have other cellular functions. We report a previously uncharacterized H. pylori type II R–M system, M.HpyAXII/R.HpyAXII. We show that this system targets GTAC sites, which are rare in the H. pylori chromosome but numerous in ribosomal RNA genes. As predicted, this type II R–M system showed attributes of a selfish element. Deletion of the methyltransferase M.HpyAXII is lethal when associated with an active endonuclease R.HpyAXII unless compensated by adaptive mutation or gene amplification. R.HpyAXII effectively restricted both unmethylated plasmid and chromosomal DNA during natural transformation and was predicted to belong to the novel ‘half pipe’ structural family of endonucleases. Analysis of a panel of clinical isolates revealed that R.HpyAXII was functional in a small number of H. pylori strains (18.9%, n = 37), whereas the activity of M.HpyAXII was highly conserved (92%, n = 50), suggesting that GTAC methylation confers a selective advantage to H. pylori. However, M.HpyAXII activity did not enhance H. pylori fitness during stomach colonization of a mouse infection model. PMID:18978016

Properties of an endonuclease activity in Micrococcus luteus acting on γ-irradiated DNA and on apurinic DNA

International Nuclear Information System (INIS)

Schaefer, G.; Haas, P.; Coquerelle, Th.; Hagen, U.

1980-01-01

A protein fraction from Micrococcus luteus with endonuclease activity against γ-irradiated DNA was isolated and characterized. An additional activity on apurinic sites could not be separated, either by sucrose gradient sedimentation or by gel filtration through Sephadex G 100. From gel filtration, a molecular weight of about 25 000 was calculated for both endonuclease activities. The endonuclease activity against γ-irradiated DNA was stimulated five-fold with 5 mM Mg ++ , whereas that against apurinic sites was less dependent on the Mg ++ concentration. 100 mM KCl inhibited the γ-ray endonuclease, but not the apurinic endonuclease activity. In γ-irradiated DNA the protein recognized 1.65 endonuclease sensitive sites per radiation-induced single-strand break, among which are 0.45 alkali labile lesions in the nucleotide strand. The was evaluated resulting in a Ksub(m)-value of 73 nM. (author)

Substrate specificity of Micrococcus luteus uv endonuclease and its overlap with DNA photolyase activity

International Nuclear Information System (INIS)

Patrick, M.H.

1975-01-01

The action of an endonuclease from Micrococcus luteus that operates on uv damage in DNA overlaps with that of DNA photolyase from yeast: homo- and heterocyclobutane dipyrimidines in DNA are substrates for both enzymes, but pyrimidine adducts or the spore photoproduct in DNA are not. As expected from this overlap, the action of the two enzymes is mutually interfering: single-strand nicks introduced by the endonuclease effectively preclude photoreactivation; conversely, formation of a photolyase-cyclobutane dipyrimidine complex can prevent nicking by the endonuclease

Properties of an endonuclease activity in Micrococcus luteus acting on. gamma. -irradiated DNA and on apurinic DNA

Energy Technology Data Exchange (ETDEWEB)

Schaefer, G; Haas, P; Coquerelle, Th; Hagen, U [Kernforschungszentrum Karlsruhe G.m.b.H. (Germany, F.R.). Inst. fuer Genetik und fuer Toxikologie von Spaltstoffen

1980-01-01

A protein fraction from Micrococcus luteus with endonuclease activity against ..gamma..-irradiated DNA was isolated and characterized. An additional activity on apurinic sites could not be separated, either by sucrose gradient sedimentation or by gel filtration through Sephadex G 100. From gel filtration, a molecular weight of about 25 000 was calculated for both endonuclease activities. The endonuclease activity against ..gamma..-irradiated DNA was stimulated five-fold with 5 mM Mg/sup + +/, whereas that against apurinic sites was less dependent on the Mg/sup + +/ concentration. 100 mM KCl inhibited the ..gamma..-ray endonuclease, but not the apurinic endonuclease activity. In ..gamma..-irradiated DNA the protein recognized 1.65 endonuclease sensitive sites per radiation-induced single-strand break, among which are 0.45 alkali labile lesions in the nucleotide strand. The was evaluated resulting in a Ksub(m)-value of 73 nM.

Output voltage calculations in double barrier magnetic tunnel junctions with asymmetric voltage behavior

KAUST Repository

Useinov, Arthur

2011-10-22

In this paper we study the asymmetric voltage behavior (AVB) of the tunnel magnetoresistance (TMR) for single and double barrier magnetic tunnel junctions (MTJs) in range of a quasi-classical free electron model. Numerical calculations of the TMR-V curves, output voltages and I-V characteristics for negative and positive values of applied voltages were carried out using MTJs with CoFeB/MgO interfaces as an example. Asymmetry of the experimental TMR-V curves is explained by different values of the minority and majority Fermi wave vectors for the left and right sides of the tunnel barrier, which arises due to different annealing regimes. Electron tunneling in DMTJs was simulated in two ways: (i) Coherent tunneling, where the DMTJ is modeled as one tunnel system and (ii) consecutive tunneling, where the DMTJ is modeled by two single barrier junctions connected in series. © 2012 Elsevier B.V. All rights reserved.

Processive nicking activity of T4 endonuclease V on UV-irradiated chromatin

International Nuclear Information System (INIS)

Gruskin, E.A.; Lloyd, R.S.

1986-01-01

T4 endonuclease V initiates the excision repair of pyrimidine dimers in UV-irradiated T4 infected E. coli cells. The pyrimidine dimer specific nicking activity of T4 endonuclease V functions by a processive scanning on UV-irradiated DNA. Previously it has been demonstrated that introduction of endonuclease V into repair-deficient human cells causes a restoration of UV survival in these cells. This demonstrates that endonuclease V is competent to incise mammalian DNA at the site of pyrimidine dimers. In order to assess the ability of endonuclease V to act processively on DNA associated as chromatin, minichromosomes were prepared for use as a substrate. Form I DNA was reconstituted with H3, H4 +/- H1 histones by sequential dialysis steps from 2.0 M NaCl to 50 mM NaCl. Time course reactions were performed with minichromosomes containing 10 and 25 dimers per molecule. In each case the rate of disappearance of form I DNA which was associated as chromatin was decreased relative to that of naked form I DNA. Concurrent with that observation, the rate and extent of appearance of form III DNA was increased with the DNA in minichromosomes relative to naked DNA. This is diagnostic of an enhancement of processivity. The inclusion of H1 in the minichromosomes resulted in a slight additional increase in processivity relative to minichromosomes consisting only of H3 and H4

Optimal inverter logic gate using 10-nm double gate-all-around (DGAA transistor with asymmetric channel width

Directory of Open Access Journals (Sweden)

Myunghwan Ryu

2016-01-01

Full Text Available We investigate the electrical characteristics of a double-gate-all-around (DGAA transistor with an asymmetric channel width using three-dimensional device simulation. The DGAA structure creates a silicon nanotube field-effect transistor (NTFET with a core-shell gate architecture, which can solve the problem of loss of gate controllability of the channel and provides improved short-channel behavior. The channel width asymmetry is analyzed on both sides of the terminals of the transistors, i.e., source and drain. In addition, we consider both n-type and p-type DGAA FETs, which are essential to forming a unit logic cell, the inverter. Simulation results reveal that, according to the carrier types, the location of the asymmetry has a different effect on the electrical properties of the devices. Thus, we propose the N/P DGAA FET structure with an asymmetric channel width to form the optimal inverter. Various electrical metrics are analyzed to investigate the benefits of the optimal inverter structure over the conventional inverter structure. Simulation results show that 27% delay and 15% leakage power improvement are enabled in the optimum structure.

The metabolic enhancer piracetam attenuates mitochondrion-specific endonuclease G translocation and oxidative DNA fragmentation.

Science.gov (United States)

Gupta, Sonam; Verma, Dinesh Kumar; Biswas, Joyshree; Rama Raju, K Siva; Joshi, Neeraj; Wahajuddin; Singh, Sarika

2014-08-01

This study was performed to investigate the involvement of mitochondrion-specific endonuclease G in piracetam (P)-induced protective mechanisms. Studies have shown the antiapoptotic effects of piracetam but the mechanism of action of piracetam is still an enigma. To assess the involvement of endonuclease G in piracetam-induced protective effects, astrocyte glial cells were treated with lipopolysaccharide (LPS) and piracetam. LPS treatment caused significantly decreased viability, mitochondrial activity, oxidative stress, chromatin condensation, and DNA fragmentation, which were attenuated by piracetam cotreatment. Cotreatment of astrocytes with piracetam showed its significantly time-dependent absorption as observed with high-performance liquid chromatography. Astrocytes treated with piracetam alone showed enhanced mitochondrial membrane potential (MMP) in comparison to control astrocytes. However, in LPS-treated cells no significant alteration in MMP was observed in comparison to control cells. Protein and mRNA levels of the terminal executor of the caspase-mediated pathway, caspase-3, were not altered significantly in LPS or LPS + piracetam-treated astrocytes, whereas endonuclease G was significantly translocated to the nucleus in LPS-treated astrocytes. Piracetam cotreatment attenuated the LPS-induced endonuclease G translocation. In conclusion this study indicates that LPS treatment of astrocytes caused decreased viability, oxidative stress, mitochondrial dysfunction, chromatin condensation, DNA damage, and translocation of endonuclease G to the nucleus, which was inhibited by piracetam cotreatment, confirming that the mitochondrion-specific endonuclease G is one of the factors involved in piracetam-induced protective mechanisms. Copyright © 2014 Elsevier Inc. All rights reserved.

Chiral Aminophosphines as Catalysts for Enantioselective Double-Michael Indoline Syntheses

Directory of Open Access Journals (Sweden)

Ohyun Kwon

2012-05-01

Full Text Available The bisphosphine-catalyzed double-Michael addition of dinucleophiles to electron-deficient acetylenes is an efficient process for the synthesis of many nitrogen-containing heterocycles. Because the resulting heterocycles contain at least one stereogenic center, this double-Michael reaction would be even more useful if an asymmetric variant of the reaction were to be developed. Aminophosphines can also facilitate the double-Michael reaction and chiral amines are more readily available in Nature and synthetically; therefore, in this study we prepared several new chiral aminophosphines. When employed in the asymmetric double-Michael reaction between ortho-tosylamidophenyl malonate and 3-butyn-2-one, the chiral aminophosphines produced indolines in excellent yields with moderate asymmetric induction.

A functional endonuclease Q exists in the bacterial domain: identification and characterization of endonuclease Q from Bacillus pumilus.

Science.gov (United States)

Shiraishi, Miyako; Ishino, Sonoko; Cann, Isaac; Ishino, Yoshizumi

2017-05-01

DNA base deamination occurs spontaneously under physiological conditions and is promoted by high temperature. Therefore, hyperthermophiles are expected to have efficient repair systems of the deaminated bases in their genomes. Endonuclease Q (EndoQ) was originally identified from the hyperthermophlic archaeon, Pyrococcus furiosus, as a hypoxanthine-specific endonuclease recently. Further biochemical analyses revealed that EndoQ also recognizes uracil, xanthine, and the AP site in DNA, and is probably involved in a specific repair process for damaged bases. Initial phylogenetic analysis showed that an EndoQ homolog is found only in the Thermococcales and some of the methanogens in Archaea, and is not present in most members of the domains Bacteria and Eukarya. A better understanding of the distribution of the EndoQ-mediated repair system is, therefore, of evolutionary interest. We showed here that an EndoQ-like polypeptide from Bacillus pumilus, belonging to the bacterial domain, is functional and has similar properties with the archaeal EndoQs.

Multiplex, rapid and sensitive isothermal detection of nucleic-acid sequence by endonuclease restriction-mediated real-time multiple cross displacement amplification

Directory of Open Access Journals (Sweden)

Yi eWang

2016-05-01

Full Text Available We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA, which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5’ end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labelled at the 5’ end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5’ end short sequences and their complementary sequences, which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 minutes, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification.

Science.gov (United States)

Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun

2016-01-01

We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5' end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5' end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

DNA Nucleotide Sequence Restricted by the RI Endonuclease

Science.gov (United States)

Hedgpeth, Joe; Goodman, Howard M.; Boyer, Herbert W.

1972-01-01

The sequence of DNA base pairs adjacent to the phosphodiester bonds cleaved by the RI restriction endonuclease in unmodified DNA from coliphage λ has been determined. The 5′-terminal nucleotide labeled with 32P and oligonucleotides up to the heptamer were analyzed from a pancreatic DNase digest. The following sequence of nucleotides adjacent to the RI break made in λ DNA was deduced from these data and from the 3′-dinucleotide sequence and nearest-neighbor analysis obtained from repair synthesis with the DNA polymerase of Rous sarcoma virus [Formula: see text] The RI endonuclease cleavage of the phosphodiester bonds (indicated by arrows) generates 5′-phosphoryls and short cohesive termini of four nucleotides, pApApTpT. The most striking feature of the sequence is its symmetry. PMID:4343974

Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses

Science.gov (United States)

Rao, Venigalla B.; Feiss, Michael

2016-01-01

Translocation of viral double-stranded DNA (dsDNA) into the icosahedral prohead shell is catalyzed by TerL, a motor protein that has ATPase, endonuclease, and translocase activities. TerL, following endonucleolytic cleavage of immature viral DNA concatemer recognized by TerS, assembles into a pentameric ring motor on the prohead’s portal vertex and uses ATP hydrolysis energy for DNA translocation. TerL’s N-terminal ATPase is connected by a hinge to the C-terminal endonuclease. Inchworm models propose that modest domain motions accompanying ATP hydrolysis are amplified, through changes in electrostatic interactions, into larger movements of the C-terminal domain bound to DNA. In phage φ29, four of the five TerL subunits sequentially hydrolyze ATP, each powering translocation of 2.5 bp. After one viral genome is encapsidated, the internal pressure signals termination of packaging and ejection of the motor. Current focus is on the structures of packaging complexes and the dynamics of TerL during DNA packaging, endonuclease regulation, and motor mechanics. PMID:26958920

Asymmetric GaAs n-type double δ-doped quantum wells as a source of intersubband-related nonlinear optical response: Effects of an applied electric field

International Nuclear Information System (INIS)

Rodríguez-Magdaleno, K.A.; Martínez-Orozco, J.C.; Rodríguez-Vargas, I.; Mora-Ramos, M.E.; Duque, C.A.

2014-01-01

In this work, the conduction band electron states and the associated intersubband-related linear and nonlinear optical absorption coefficient and relative refractive index change are calculated for an asymmetric double n-type δ-doped quantum well in a GaAs-matrix. The effects of an external applied static electric field are included. Values of the two-dimensional impurities density (N 2d ) of each single δ-doped quantum well are taken to vary within the range of 1.0×10 12 to 7.0×10 12 cm −2 , consistent with the experimental data growth regime. The optical responses are reported as a function of the δ-doped impurities density and the applied electric field. It is shown that single electron states and the related optical quantities are significantly affected by the structural asymmetry of the double δ-doped quantum well system. In addition, a brief comparison with the free-carrier-related optical response is presented. -- Highlights: • Nonlinear optics in asymmetric double n-type δ-doped quantum well in a GaAs-matrix. • The system is considered under external applied electric field in growth direction. • The 2D impurity density is consistent with the experimental data growth regime. • The optical quantities are significantly affected by the structural asymmetry of the system

Asymmetric GaAs n-type double δ-doped quantum wells as a source of intersubband-related nonlinear optical response: Effects of an applied electric field

Energy Technology Data Exchange (ETDEWEB)

Rodríguez-Magdaleno, K.A.; Martínez-Orozco, J.C.; Rodríguez-Vargas, I. [Unidad Académica de Física, Universidad Autónoma de Zacatecas, Calz. Solidaridad Esq. Paseo a La Bufa S/N. C.P. 98060 Zacatecas (Mexico); Mora-Ramos, M.E. [Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, CP 62209 Cuernavaca, Morelos (Mexico); Física Teórica y Aplicada, Escuela de Ingeniería de Antioquia, AA 7516 Medellín (Colombia); Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Duque, C.A., E-mail: cduque@fisica.udea.edu.co [Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia)

2014-03-15

In this work, the conduction band electron states and the associated intersubband-related linear and nonlinear optical absorption coefficient and relative refractive index change are calculated for an asymmetric double n-type δ-doped quantum well in a GaAs-matrix. The effects of an external applied static electric field are included. Values of the two-dimensional impurities density (N{sub 2d}) of each single δ-doped quantum well are taken to vary within the range of 1.0×10{sup 12} to 7.0×10{sup 12} cm{sup −2}, consistent with the experimental data growth regime. The optical responses are reported as a function of the δ-doped impurities density and the applied electric field. It is shown that single electron states and the related optical quantities are significantly affected by the structural asymmetry of the double δ-doped quantum well system. In addition, a brief comparison with the free-carrier-related optical response is presented. -- Highlights: • Nonlinear optics in asymmetric double n-type δ-doped quantum well in a GaAs-matrix. • The system is considered under external applied electric field in growth direction. • The 2D impurity density is consistent with the experimental data growth regime. • The optical quantities are significantly affected by the structural asymmetry of the system.

Comparison of genomes of malignant catarrhal fever-associated herpesviruses by restriction endonuclease analysis.

Science.gov (United States)

Shih, L M; Zee, Y C; Castro, A E

1989-01-01

The restriction endonuclease DNA cleavage patterns of eight isolates of malignant catarrhal fever-associated herpesviruses were examined using the restriction endonucleases HindIII and EcoRI. The eight viruses could be assigned to two distinct groups. Virus isolates from a blue wildebeest, a sika deer and an ibex had restriction endonuclease DNA cleavage patterns that were in general similar to each other. The restriction pattern of these three viruses was distinct from the other five. Of these five, four were isolated from a greater kudu, a white tailed wildebeest, a white bearded wildebeest, and a cape hartebeest. The fifth isolate C500, was isolated from a domestic cow with malignant catarrhal fever. These five viruses had similar DNA cleavage patterns.

Excision repair of gamma-ray-induced alkali-stable DNA lesions with the help of γ-endonuclease from Micrococcus luteus

International Nuclear Information System (INIS)

Tomilin, N.V.; Barenfeld, L.S.

1979-01-01

γ-endonuclease Y, an enzyme that hydrolyses phosphodiester bonds at alkali-stable lesions in γ-irradiated (N 2 , tris buffer) DNA, has been partially purified from Micrococcus luteus. The enzyme has a molecular weight of about 19 000, induces single-strand breaks with 3'OH-5'PO 4 termini and contains endonuclease activity towards DNA treated with 7-bromomethylbenz(a)anthracene. γ-endonuclease Y induces breaks in OsO 4 -treated poly(dA-dT) and apparently is specific towards γ-ray-induced base lesions of the t' type. The complete excision repair of γ-endonuclease Y substrate sites has been performed in vitro by γ-endonuclease Y, DNA polymerase and ligase. (author)

Excision repair of gamma-ray-induced alkali-stable DNA lesions with the help of. gamma. -endonuclease from Micrococcus luteus

Energy Technology Data Exchange (ETDEWEB)

Tomilin, N V; Barenfeld, L S [AN SSSR, Leningrad. Inst. Tsitologii

1979-03-01

..gamma..-endonuclease Y, an enzyme that hydrolyses phosphodiester bonds at alkali-stable lesions in ..gamma..-irradiated (N/sub 2/, tris buffer) DNA, has been partially purified from Micrococcus luteus. The enzyme has a molecular weight of about 19 000, induces single-strand breaks with 3'OH-5'PO/sub 4/ termini and contains endonuclease activity towards DNA treated with 7-bromomethylbenz(a)anthracene. ..gamma..-endonuclease Y induces breaks in OsO/sub 4/-treated poly(dA-dT) and apparently is specific towards ..gamma..-ray-induced base lesions of the t' type. The complete excision repair of ..gamma..-endonuclease Y substrate sites has been performed in vitro by ..gamma..-endonuclease Y, DNA polymerase and ligase.

DENV gene of bacteriophage T4 codes for both pyrimidine dimer-DNA glycosylase and apyrimidinic endonuclease activities

International Nuclear Information System (INIS)

McMillan, S.; Edenberg, H.J.; Radany, E.H.; Friedberg, R.C.; Friedberg, E.C.

1981-01-01

Recent studies have shown that purified preparations of phage T4 UV DNA-incising activity (T4 UV endonuclease or endonuclease V of phase T4) contain a pyrimidine dimer-DNA glycosylase activity that catalyzes hydrolysis of the 5' glycosyl bond of dimerized pyrimidines in UV-irradiated DNA. Such enzyme preparations have also been shown to catalyze the hydrolysis of phosphodiester bonds in UV-irradiated DNA at a neutral pH, presumably reflecting the action of an apurinic/apyrimidinic endonuclease at the apyrimidinic sites created by the pyrimidine dimer-DNA glycosylase. In this study we found that preparations of T4 UV DNA-incising activity contained apurinic/apyrimidinic endonuclease activity that nicked depurinated form I simian virus 40 DNA. Apurinic/apyrimidinic endonuclease activity was also found in extracts of Escherichia coli infected with T4 denV + phage. Extracts of cells infected with T4 denV mutants contained significantly lower levels of apurinic/apyrimidinic endonuclease activity; these levels were no greater than the levels present in extracts of uninfected cells. Furthermore, the addition of DNA containing UV-irradiated DNA and T4 enzyme resulted in competition for pyrimidine dimer-DNA glycosylase activity against the UV-irradiated DNA. On the basis of these results, we concluded that apurinic/apyrimidinic endonuclease activity is encoded by the denV gene of phage T4, the same gene that codes for pyrimidine dimer-DNA glycosylase activity

Intratarsal fixation at the same level as the skin incision to reduce asymmetric double eyelids: evaluation of symmetry using photogrammetry.

Science.gov (United States)

Han, Kihwan; Yeo, Hyeonjung; Choi, Tae Hyun; Son, Daegu; Kim, Jun Hyung

2010-03-01

One of the most common complications of double eyelid operations is asymmetry. To reduce asymmetry, we fixed the dermis to the tarsal plate at the same level as the skin incision, and objectively evaluated the symmetry of the height using photogrammetry.Of 30 patients who had double eyelid operations by the intratarsal fixation technique, 15 patients completed a minimum follow-up of 6 months. After the skin incision and removal of the orbicularis oculi muscle and the orbital fat, the pretarsal fat pad was excised to expose the superior portion of the tarsal plate. The 3 fixation points were marked on the tarsal plate at the same level with the skin incision using a spreading caliper. The dermis was fixed to the marked points of the tarsal plate and the skin was closed.The height of the double eyelid was measured by clinical photography at 4 points when the eyes were opened and at 3 points when the eyes were closed. The height proportional index at each point was obtained by dividing the height of the left double eyelid by that of the right double eyelid. We compared each height proportional index with "1" to evaluate the symmetry of both double eyelids using a paired t test.The follow-up period was an average of 9.0 months. The mean height proportional indices were 0.97 (a), 0.96 (b), 0.98 (c), 1.08 (d), 0.97 (e), 1.02 (f), and 1.13 (g). According to a paired t test, the height of the left double eyelid was not different from that of the right double eyelid.Intratarsal fixation, along with other previously known methods, decreases asymmetric double eyelids.

Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

Energy Technology Data Exchange (ETDEWEB)

Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A., E-mail: alashkov83@gmail.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2012-05-15

Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

Science.gov (United States)

Sternberg, Samuel H; Redding, Sy; Jinek, Martin; Greene, Eric C; Doudna, Jennifer A

2014-03-06

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

Science.gov (United States)

Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

2014-03-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

Germline excision of transgenes in Aedes aegypti by homing endonucleases.

Science.gov (United States)

Aryan, Azadeh; Anderson, Michelle A E; Myles, Kevin M; Adelman, Zach N

2013-01-01

Aedes (Ae.) aegypti is the primary vector for dengue viruses (serotypes1-4) and chikungunya virus. Homing endonucleases (HEs) are ancient selfish elements that catalyze double-stranded DNA breaks (DSB) in a highly specific manner. In this report, we show that the HEs Y2-I-AniI, I-CreI and I-SceI are all capable of catalyzing the excision of genomic segments from the Ae. aegypti genome in a heritable manner. Y2-I-AniI demonstrated the highest efficiency at two independent genomic targets, with 20-40% of Y2-I-AniI-treated individuals producing offspring that had lost the target transgene. HE-induced DSBs were found to be repaired via the single-strand annealing (SSA) and non-homologous end-joining (NHEJ) pathways in a manner dependent on the availability of direct repeat sequences in the transgene. These results support the development of HE-based gene editing and gene drive strategies in Ae. aegypti, and confirm the utility of HEs in the manipulation and modification of transgenes in this important vector.

Characterization of DNA substrate specificities of apurinic/apyrimidinic endonucleases from Mycobacterium tuberculosis.

Science.gov (United States)

Abeldenov, Sailau; Talhaoui, Ibtissam; Zharkov, Dmitry O; Ishchenko, Alexander A; Ramanculov, Erlan; Saparbaev, Murat; Khassenov, Bekbolat

2015-09-01

Apurinic/apyrimidinic (AP) endonucleases are key enzymes involved in the repair of abasic sites and DNA strand breaks. Pathogenic bacteria Mycobacterium tuberculosis contains two AP endonucleases: MtbXthA and MtbNfo members of the exonuclease III and endonuclease IV families, which are exemplified by Escherichia coli Xth and Nfo, respectively. It has been shown that both MtbXthA and MtbNfo contain AP endonuclease and 3'→5' exonuclease activities. However, it remains unclear whether these enzymes hold 3'-repair phosphodiesterase and nucleotide incision repair (NIR) activities. Here, we report that both mycobacterial enzymes have 3'-repair phosphodiesterase and 3'-phosphatase, and MtbNfo contains in addition a very weak NIR activity. Interestingly, depending on pH, both enzymes require different concentrations of divalent cations: 0.5mM MnCl2 at pH 7.6 and 10 mM at pH 6.5. MtbXthA requires a low ionic strength and 37 °C, while MtbNfo requires high ionic strength (200 mM KCl) and has a temperature optimum at 60 °C. Point mutation analysis showed that D180 and N182 in MtbXthA and H206 and E129 in MtbNfo are critical for enzymes activities. The steady-state kinetic parameters indicate that MtbXthA removes 3'-blocking sugar-phosphate and 3'-phosphate moieties at DNA strand breaks with an extremely high efficiency (kcat/KM=440 and 1280 μM(-1)∙min(-1), respectively), while MtbNfo exhibits much lower 3'-repair activities (kcat/KM=0.26 and 0.65 μM(-1)∙min(-1), respectively). Surprisingly, both MtbXthA and MtbNfo exhibited very weak AP site cleavage activities, with kinetic parameters 100- and 300-fold lower, respectively, as compared with the results reported previously. Expression of MtbXthA and MtbNfo reduced the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to methylmethanesulfonate and H2O2 to various degrees. Taken together, these data establish the DNA substrate specificity of M. tuberculosis AP endonucleases and suggest their possible role

Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels.

Science.gov (United States)

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P; Khun, Joelle; Vos, Marten H; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-05-04

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction.

Modulation of the Pyrococcus abyssi NucS Endonuclease Activity by Replication Clamp at Functional and Structural Levels*

Science.gov (United States)

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P.; Khun, Joelle; Vos, Marten H.; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-01-01

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5′ and 3′ flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction. PMID:22431731

A new endonuclease recognizing the deoxynucleotide sequence CCNNGG from the cyanobacterium Synechocystis 6701.

Science.gov (United States)

Calléja, F; Tandeau de Marsac, N; Coursin, T; van Ormondt, H; de Waard, A

1985-09-25

A new sequence-specific endonuclease from the cyanobacterium Synechocystis species PCC 6701 has been purified and characterized. This enzyme, SecI, is unique in recognizing the nucleotide sequence: 5' -CCNNGG-3' 3' -GGNNCC-5' and cleaves it at the position indicated by the symbol. Two other restriction endonucleases, SecII and SecIII, found in this organism are isoschizomers of MspI and MstII, respectively.

PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance.

Science.gov (United States)

van Oers, Johanna M M; Roa, Sergio; Werling, Uwe; Liu, Yiyong; Genschel, Jochen; Hou, Harry; Sellers, Rani S; Modrich, Paul; Scharff, Matthew D; Edelmann, Winfried

2010-07-27

The DNA mismatch repair protein PMS2 was recently found to encode a novel endonuclease activity. To determine the biological functions of this activity in mammals, we generated endonuclease-deficient Pms2E702K knock-in mice. Pms2EK/EK mice displayed increased genomic mutation rates and a strong cancer predisposition. In addition, class switch recombination, but not somatic hypermutation, was impaired in Pms2EK/EK B cells, indicating a specific role in Ig diversity. In contrast to Pms2-/- mice, Pms2EK/EK male mice were fertile, indicating that this activity is dispensable in spermatogenesis. Therefore, the PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance and tumor suppression.

Adenosine triphosphate stimulates Aquifex aeolicus MutL endonuclease activity.

Directory of Open Access Journals (Sweden)

Jerome Mauris

2009-09-01

Full Text Available Human PMS2 (hPMS2 homologues act to nick 5' and 3' to misincorporated nucleotides during mismatch repair in organisms that lack MutH. Mn(++ was previously found to stimulate the endonuclease activity of these homologues. ATP was required for the nicking activity of hPMS2 and yPMS1, but was reported to inhibit bacterial MutL proteins from Thermus thermophilus and Aquifex aeolicus that displayed homology to hPMS2. Mutational analysis has identified the DQHA(X(2E(X(4E motif present in the C-terminus of PMS2 homologues as important for endonuclease activity.We examined the effect ATP had on the Mn(++ induced nicking of supercoiled pBR322 by full-length and mutant A. aeolicus MutL (Aae MutL proteins. Assays were single time point, enzyme titration experiments or reaction time courses. The maximum velocity for MutL nicking was determined to be 1.6+/-0.08x10(-5 s(-1 and 4.2+/-0.3x10(-5 s(-1 in the absence and presence of ATP, respectively. AMPPNP stimulated the nicking activity to a similar extent as ATP. A truncated Aae MutL protein composed of only the C-terminal 123 amino acid residues was found to nick supercoiled DNA. Furthermore, mutations in the conserved C-terminal DQHA(X(2E(X(4E and CPHGRP motifs were shown to abolish Aae MutL endonuclease activity.ATP stimulated the Mn(++ induced endonuclease activity of Aae MutL. Experiments utilizing AMPPNP implied that the stimulation did not require ATP hydrolysis. A mutation in the DQHA(X(2E(X(4E motif of Aae MutL further supported the role of this region in endonclease activity. For the first time, to our knowledge, we demonstrate that changing the histidine residue in the conserved CPHGRP motif abolishes endonucleolytic activity of a hPMS2 homologue. Finally, the C-terminal 123 amino acid residues of Aae MutL were sufficient to display Mn(++ induced nicking activity.

Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species.

Science.gov (United States)

Posey, Karen L; Koufopanou, Vassiliki; Burt, Austin; Gimble, Frederick S

2004-01-01

Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit to their host. They encode site-specific DNA endonucleases that perpetuate the element within a species population by homing and disseminate it between species by horizontal transfer. Several yeast species contain the VMA1 HEG that encodes the intein-associated VMA1-derived endonuclease (VDE). The evolutionary state of VDEs from 12 species was assessed by assaying their endonuclease activities. Only two enzymes are active, PI-ZbaI from Zygosaccharomyces bailii and PI-ScaI from Saccharomyces cariocanus. PI-ZbaI cleaves the Z.bailii recognition sequence significantly faster than the Saccharomyces cerevisiae site, which differs at six nucleotide positions. A mutational analysis indicates that PI-ZbaI cleaves the S.cerevisiae substrate poorly due to the absence of a contact that is analogous to one made in PI-SceI between Gln-55 and nucleotides +9/+10. PI-ZbaI cleaves the Z.bailii substrate primarily due to a single base-pair substitution (A/T+5 --> T/A+5). Structural modeling of the PI-ZbaI/DNA complex suggests that Arg-331, which is absent in PI-SceI, contacts T/A+5, and the reduced activity observed in a PI-ZbaI R331A mutant provides evidence for this interaction. These data illustrate that homing endonucleases evolve altered specificity as they adapt to recognize alternative target sites.

Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species

Science.gov (United States)

Posey, Karen L.; Koufopanou, Vassiliki; Burt, Austin; Gimble, Frederick S.

2004-01-01

Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit to their host. They encode site-specific DNA endonucleases that perpetuate the element within a species population by homing and disseminate it between species by horizontal transfer. Several yeast species contain the VMA1 HEG that encodes the intein-associated VMA1-derived endonuclease (VDE). The evolutionary state of VDEs from 12 species was assessed by assaying their endonuclease activities. Only two enzymes are active, PI-ZbaI from Zygosaccharomyces bailii and PI-ScaI from Saccharomyces cariocanus. PI-ZbaI cleaves the Z.bailii recognition sequence significantly faster than the Saccharomyces cerevisiae site, which differs at six nucleotide positions. A mutational analysis indicates that PI-ZbaI cleaves the S.cerevisiae substrate poorly due to the absence of a contact that is analogous to one made in PI-SceI between Gln-55 and nucleotides +9/+10. PI-ZbaI cleaves the Z.bailii substrate primarily due to a single base-pair substitution (A/T+5 → T/A+5). Structural modeling of the PI-ZbaI/DNA complex suggests that Arg-331, which is absent in PI-SceI, contacts T/A+5, and the reduced activity observed in a PI-ZbaI R331A mutant provides evidence for this interaction. These data illustrate that homing endonucleases evolve altered specificity as they adapt to recognize alternative target sites. PMID:15280510

Development of ion-acoustic double layers through ion-acoustic fluctuations

International Nuclear Information System (INIS)

Sekar, A.N.; Saxena, Y.C.

1985-01-01

Experimental results on the formation of ion acoustic double layers resembling asymmetric ion-holes are presented. In a double plasma device, modified suitably to inject electron beam into the target plasma, modulation of the beam through step potential leads to excitation of ion-acoustic fluctuation. The ion-acoustic fluctuation, growing away from the grids separating source and target plasmas, developed into weak asymmetric ion-acoustic double layer. The observations are in qualitative agreement with theoretical models and computer simulations. (author)

Sequence specificity of DNA cleavage by Micrococcus luteus γ endonuclease

International Nuclear Information System (INIS)

Hentosh, P.; Henner, W.D.; Reynolds, R.J.

1985-01-01

DNA fragments of defined sequence have been used to determine the sites of cleavage by γ-endonuclease activity in extracts prepared from Micrococcus luteus. End-labeled DNA restriction fragments of pBR322 DNA that had been irradiated under nitrogen in the presence of potassium iodide or t-butanol were treated with M. luteus γ endonuclease and analyzed on irradiated DNA preferentially at the positions of cytosines and thymines. DNA cleavage occurred immediately to the 3' side of pyrimidines in irradiated DNA and resulted in fragments that terminate in a 5'-phosphoryl group. These studies indicate that both altered cytosines and thymines may be important DNA lesions requiring repair after exposure to γ radiation

Expression analysis of a ''Cucurbita'' cDNA encoding endonuclease

International Nuclear Information System (INIS)

Szopa, J.

1995-01-01

The nuclear matrices of plant cell nuclei display intrinsic nuclease activity which consists in nicking supercoiled DNA. A cDNA encoding a 32 kDa endonuclease has been cloned and sequenced. The nucleotide and deduced amino-acid sequences show high homology to known 14-3-3-protein sequences from other sources. The amino-acid sequence shows agreement with consensus sequences for potential phosphorylation by protein kinase A and C and for calcium, lipid and membrane-binding sites. The nucleotide-binding site is also present within the conserved part of the sequence. By Northern blot analysis, the differential expression of the corresponding mRNA was detected; it was the strongest in sink tissues. The endonuclease activity found on DNA-polyacrylamide gel electrophoresis coincided with mRNA content and was the highest in tuber. (author). 22 refs, 6 figs

Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.

Science.gov (United States)

Tóth, Eszter; Huszár, Krisztina; Bencsura, Petra; Kulcsár, Péter István; Vodicska, Barbara; Nyeste, Antal; Welker, Zsombor; Tóth, Szilvia; Welker, Ervin

2014-01-01

The procedure described here allows the cloning of PCR fragments containing a recognition site of the restriction endonuclease (Type IIP) used for cloning in the sequence of the insert. A Type IIS endonuclease--a Body Double of the Type IIP enzyme--is used to generate the same protruding palindrome. Thus, the insert can be cloned to the Type IIP site of the vector without digesting the PCR product with the same Type IIP enzyme. We achieve this by incorporating the recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of its recognition site in the PCR primer in such a way that the cutting positions straddle the desired overhang sequence. Digestion of the PCR product by the Body Double generates the required overhang. Hitherto the use of Type IIS restriction enzymes in cloning reactions has only been used for special applications, the approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for general cloning purposes. To assist in finding Body Double enzymes, we summarised the available Type IIS enzymes which are potentially useful for Body Double cloning and created an online program (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection of suitable Body Double enzymes and the design of the appropriate primers.

Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes.

Energy Technology Data Exchange (ETDEWEB)

Tsutakawa, Susan E.; Shin, David S.; Mol, Clifford D.; Izum, Tadahide; Arvai, Andrew S.; Mantha, Anil K.; Szczesny, Bartosz; Ivanov, Ivaylo N.; Hosfield, David J.; Maiti, Buddhadev; Pique, Mike E.; Frankel, Kenneth A.; Hitomi, Kenichi; Cunningham, Richard P.; Mitra, Sankar; Tainer, John A.

2013-03-22

Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair, AP sites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 ? resolution APE1-DNA product complex with Mg(2+) and a 0.92 Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize key APE1 catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg(2+). Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.

Asymmetric biosynthesis of (1S, 2S)-ephedrine by Morganella ...

African Journals Online (AJOL)

STORAGESEVER

2009-02-18

>99% ee) and 84.4% molar yield. ... field of synthetic chemistry, which overlaps both organic chemistry ... that possess asymmetric synthesis abilities have been ..... erythropolis, and its application to double chiral compound.

Murine leukemia virus pol gene products: analysis with antisera generated against reverse transcriptase and endonuclease fusion proteins expressed in Escherichia coli

International Nuclear Information System (INIS)

Hu, S.C.; Court, D.L.; Zweig, M.; Levin, J.G.

1986-01-01

The organization of the murine leukemia virus (MuLV) pol gene was investigated by expressing molecular clones containing AKR MuLV reverse transcriptase or endonuclease or both gene segments in Escherichia coli and generating specific antisera against the expressed bacterial proteins. Reaction of these antisera with detergent-disrupted virus precipitated and 80-kilodalton (kDa) protein, the MuLV reverse transcriptase, and a 46-kDa protein which we believe is the viral endonuclease. A third (50-kDa) protein, related to reverse transcriptase, was also precipitated. Bacterial extracts of clones expressing reverse transcriptase and endonuclease sequences competed with the viral 80- and 46-kDa proteins, respectively. These results demonstrate that the antisera are specific for viral reverse transcriptase and endonuclease. Immunoprecipitation of AKR MuLV with antisera prepared against a bacterial protein containing only endonuclease sequences led to the observation that reverse transcriptase and endonuclease can be associated as a complex involving a disulfide bond(s)

Physical association of pyrimidine dimer DNA glycosylase and apurinic/apyrimidinic DNA endonuclease essential for repair of ultraviolet-damaged DNA

International Nuclear Information System (INIS)

Nakabeppu, Y.; Sekiguchi, M.

1981-01-01

T4 endonuclease, which is involved in repair of uv-damaged DNA, has been purified to apparent physical homogeneity. Incubation of uv-irradiated poly(dA).poly(dT) with the purified enzyme preparations resulted in production of alkali-labile apyrimidinic sites, followed by formation of nicks in the polymer. By performing a limited reaction with T4 endonuclease V at pH 8.5, irradiated polymer was converted to an intermediate form that carried a large number of alkali-labile sites but only a few nicks. The intermediate was used as substrate for the assay of apurinic/apyrimidinic DNA endonuclease activity. The two activities, a pyrimidine dimer DNA glycosylase and an apurinic/apyrimidinic DNA endonuclease, were copurified and found in enzyme preparations that contained only a 16,000-dalton polypeptide. These results strongly suggested that a DNA glycosylase specific for pyrimidine dimers and an apurinic/apyrimidinic DNA endonuclease reside in a single polypeptide chain coded by the denV gene of bacteriophage T4

Asymmetric Synthesis of Apratoxin E.

Science.gov (United States)

Mao, Zhuo-Ya; Si, Chang-Mei; Liu, Yi-Wen; Dong, Han-Qing; Wei, Bang-Guo; Lin, Guo-Qiang

2016-10-21

An efficient method for asymmetric synthesis of apratoxin E 2 is described in this report. The chiral lactone 8, recycled from the degradation of saponin glycosides, was utilized to prepare the non-peptide fragment 6. In addition to this "from nature to nature" strategy, olefin cross-metathesis (CM) was applied as an alternative approach for the formation of the double bond. Moreover, pentafluorophenyl diphenylphosphinate was found to be an efficient condensation reagent for the macrocyclization.

The asymmetric reactions of mean and volatility of stock returns to domestic and international information based on a four-regime double-threshold GARCH model

Science.gov (United States)

Chen, Cathy W. S.; Yang, Ming Jing; Gerlach, Richard; Jim Lo, H.

2006-07-01

In this paper, we investigate the asymmetric reactions of mean and volatility of stock returns in five major markets to their own local news and the US information via linear and nonlinear models. We introduce a four-regime Double-Threshold GARCH (DTGARCH) model, which allows asymmetry in both the conditional mean and variance equations simultaneously by employing two threshold variables, to analyze the stock markets’ reactions to different types of information (good/bad news) generated from the domestic markets and the US stock market. By applying the four-regime DTGARCH model, this study finds that the interaction between the information of domestic and US stock markets leads to the asymmetric reactions of stock returns and their variability. In addition, this research also finds that the positive autocorrelation reported in the previous studies of financial markets may in fact be mis-specified, and actually due to the local market's positive response to the US stock market.

Asymmetric strand segregation: epigenetic costs of genetic fidelity?

Directory of Open Access Journals (Sweden)

Diane P Genereux

2009-06-01

Full Text Available Asymmetric strand segregation has been proposed as a mechanism to minimize effective mutation rates in epithelial tissues. Under asymmetric strand segregation, the double-stranded molecule that contains the oldest DNA strand is preferentially targeted to the somatic stem cell after each round of DNA replication. This oldest DNA strand is expected to have fewer errors than younger strands because some of the errors that arise on daughter strands during their synthesis fail to be repaired. Empirical findings suggest the possibility of asymmetric strand segregation in a subset of mammalian cell lineages, indicating that it may indeed function to increase genetic fidelity. However, the implications of asymmetric strand segregation for the fidelity of epigenetic information remain unexplored. Here, I explore the impact of strand-segregation dynamics on epigenetic fidelity using a mathematical-modelling approach that draws on the known molecular mechanisms of DNA methylation and existing rate estimates from empirical methylation data. I find that, for a wide range of starting methylation densities, asymmetric -- but not symmetric -- strand segregation leads to systematic increases in methylation levels if parent strands are subject to de novo methylation events. I found that epigenetic fidelity can be compromised when enhanced genetic fidelity is achieved through asymmetric strand segregation. Strand segregation dynamics could thus explain the increased DNA methylation densities that are observed in structured cellular populations during aging and in disease.

Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus

OpenAIRE

Kiyonari, Shinichi; Tahara, Saki; Shirai, Tsuyoshi; Iwai, Shigenori; Ishino, Sonoko; Ishino, Yoshizumi

2009-01-01

Apurinic/apyrimidinic (AP) sites are the most frequently found mutagenic lesions in DNA, and they arise mainly from spontaneous base loss or modified base removal by damage-specific DNA glycosylases. AP sites are cleaved by AP endonucleases, and the resultant gaps in the DNA are repaired by DNA polymerase/DNA ligase reactions. We identified the gene product that is responsible for the AP endonuclease activity in the hyperthermophilic euryarchaeon, Pyrococcus furiosus. Furthermore, we detected...

Modulation of the DNA scanning activity of the Micrococcus luteus UV endonuclease

International Nuclear Information System (INIS)

Hamilton, R.W.; Lloyd, R.S.

1989-01-01

Micrococcus luteus UV endonuclease incises DNA at the sites of ultraviolet (UV) light-induced pyrimidine dimers. The mechanism of incision has been previously shown to be a glycosylic bond cleavage at the 5'-pyrimidine of the dimer followed by an apyrimidine endonuclease activity which cleaves the phosphodiester backbone between the pyrimidines. The process by which M. luteus UV endonuclease locates pyrimidine dimers within a population of UV-irradiated plasmids was shown to occur, in vitro, by a processive or sliding mechanism on non-target DNA as opposed to a distributive or random hit mechanism. Form I plasmid DNA containing 25 dimers per molecule was incubated with M. luteus UV endonuclease in time course reactions. The three topological forms of plasmid DNA generated were analyzed by agarose gel electrophoresis. When the enzyme encounters a pyrimidine dimer, it is significantly more likely to make only the glycosylase cleavage as opposed to making both the glycosylic and phosphodiester bond cleavages. Thus, plasmids are accumulated with many alkaline-labile sites relative to single-stranded breaks. In addition, reactions were performed at both pH 8.0 and pH 6.0, in the absence of NaCl, as well as 25,100, and 250 mM NaCl. The efficiency of the DNA scanning reaction was shown to be dependent on both the ionic strength and pH of the reaction. At low ionic strengths, the reaction was shown to proceed by a processive mechanism and shifted to a distributive mechanism as the ionic strength of the reaction increased. Processivity at pH 8.0 is shown to be more sensitive to increases in ionic strength than reactions performed at pH 6.0

DNA scanning mechanism of T4 endonuclease V. Effect of NaCl concentration on processive nicking activity

International Nuclear Information System (INIS)

Gruskin, E.A.; Lloyd, R.S.

1986-01-01

T4 endonuclease V is a pyrimidine dimer-specific endonuclease which generates incisions in DNA at the sites of pyrimidine dimers by a processive reaction mechanism. A model is presented in which the degree of processivity is directly related to the efficacy of the one-dimensional diffusion of endonuclease V on DNA by which the enzyme locates pyrimidine dimers. The modulation of the processive nicking activity of T4 endonuclease V on superhelical covalently closed circular DNA (form I) which contains pyrimidine dimers has been investigated as a function of the ionic strength of the reaction. Agarose gel electrophoresis was used to separate the three topological forms of the DNA which were generated in time course reactions of endonuclease V with dimer-containing form I DNA in the absence of NaCl, and in 25, 50, and 100 mM NaCl. The degree of processivity was evaluated in terms of the mass fraction of form III (linear) DNA which was produced as a function of the fraction of form I DNA remaining. Processivity is maximal in the absence of NaCl and decreases as the NaCl concentration is increased. At 100 mM NaCl, processivity is abolished and endonuclease V generates incisions in DNA at the site of dimers by a distributive reaction mechanism. The change from the distributive to a processive reaction mechanism occurs at NaCl concentrations slightly below 50 mM. The high degree of processivity which is observed in the absence of NaCl is reversible to the distributive mechanism, as demonstrated by experiments in which the NaCl concentration was increased during the time course reaction. In addition, unirradiated DNA inhibited the incision of irradiated DNA only at NaCl concentrations at which processivity was observed

Type II restriction endonucleases--a historical perspective and more.

Science.gov (United States)

Pingoud, Alfred; Wilson, Geoffrey G; Wende, Wolfgang

2014-07-01

This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The limits of the electron optical parameters of asymmetric double pipecol magnetic objective lenses

International Nuclear Information System (INIS)

Al-khashab, A. M.; Abas, K. A.

1997-01-01

The asymmetrical magnetic electron lens is of great importance for the electron microscopes intended for high resolution. Such lenses are determined not only by its geometric structure and shape parameters but also by the gap width to bore diameter (S/D) of its pole pieces. a systematic investigation has been carried out for asymmetric objective lenses having different bore diameters. The results indicate that the op per h ore diameter of pole piece lens has considerable effects on the electron optical properties. The Comparison between the two sets of the family of asymmetric lenses provides good performance, and suggests that the ratio of the lens gap width to the bore diameters of its pole pieces (S/ D 1 /D 2 =3) are favourable. (authors). 9 refs., 9 figs

Home and away- the evolutionary dynamics of homing endonucleases

Directory of Open Access Journals (Sweden)

Barzel Adi

2011-11-01

Full Text Available Abstract Background Homing endonucleases (HEases are a large and diverse group of site-specific DNAases. They reside within self-splicing introns and inteins, and promote their horizontal dissemination. In recent years, HEases have been the focus of extensive research due to their promising potential use in gene targeting procedures for the treatment of genetic diseases and for the genetic engineering of crop, animal models and cell lines. Results Using mathematical analysis and computational modeling, we present here a novel account for the evolution and population dynamics of HEase genes (HEGs. We describe HEGs as paradoxical selfish elements whose long-term persistence in a single population relies on low transmission rates and a positive correlation between transmission efficiency and toxicity. Conclusion Plausible conditions allow HEGs to sustain at high frequency through long evolutionary periods, with the endonuclease frequency being either at equilibrium or periodically oscillating. The predictions of our model may prove important not only for evolutionary theory but also for gene therapy and bio-engineering applications of HEases.

Effect of asymmetrical double-pockets and gate-drain underlap on Schottky barrier tunneling FET: Ambipolar conduction vs. high frequency performance

Science.gov (United States)

Shaker, Ahmed; Ossaimee, Mahmoud; Zekry, A.

2016-08-01

In this paper, a proposed structure based on asymmetrical double pockets SB-TFET with gate-drain underlap is presented. 2D extensive modeling and simulation, using Silvaco TCAD, were carried out to study the effect of both underlap length and pockets' doping on the transistor performance. It was found that the underlap from the drain side suppresses the ambipolar conduction and doesn't enhance the high-frequency characteristics. The enhancement of the high-frequency characteristics could be realized by increasing the doping of the drain pocket over the doping of the source pocket. An optimum choice was found which gives the conditions of minimum ambipolar conduction, maximum ON current and maximum cut-off frequency. These enhancements render the device more competitive as a nanometer transistor.

Short-channel drain current model for asymmetric heavily/lightly ...

Indian Academy of Sciences (India)

The paper presents a drain current model for double gate metal oxide semiconductor field effect transistors (DG MOSFETs) based on a new velocity saturation model that accounts for short-channel velocity saturation effect independently in the front and the back gate controlled channels under asymmetric front and back ...

Asymmetric double-image encryption method by using iterative phase retrieval algorithm in fractional Fourier transform domain

Science.gov (United States)

Sui, Liansheng; Lu, Haiwei; Ning, Xiaojuan; Wang, Yinghui

2014-02-01

A double-image encryption scheme is proposed based on an asymmetric technique, in which the encryption and decryption processes are different and the encryption keys are not identical to the decryption ones. First, a phase-only function (POF) of each plain image is retrieved by using an iterative process and then encoded into an interim matrix. Two interim matrices are directly modulated into a complex image by using the convolution operation in the fractional Fourier transform (FrFT) domain. Second, the complex image is encrypted into the gray scale ciphertext with stationary white-noise distribution by using the FrFT. In the encryption process, three random phase functions are used as encryption keys to retrieve the POFs of plain images. Simultaneously, two decryption keys are generated in the encryption process, which make the optical implementation of the decryption process convenient and efficient. The proposed encryption scheme has high robustness to various attacks, such as brute-force attack, known plaintext attack, cipher-only attack, and specific attack. Numerical simulations demonstrate the validity and security of the proposed method.

Presence of UV-endonuclease sensitive sites in daughter DNA of UV-irradiated mammalian cells

International Nuclear Information System (INIS)

D'Ambrosio, S.; Setlow, R.B.

1978-02-01

Asynchronous Chinese hamster cells were irradiated with 10 Jm -2 uv radiation and 0.25 to 4 hours later pulse-labeled with [ 3 H]thymidine. Cells synchronized by shaking off mitotic and G 1 cells were irradiated in either the G 1 -phase or S-phase of the cell cycle and pulse-labeled with [ 3 H]thymidine in the S-phase. After a 12 to 14 hour chase in unlabeled medium, the DNA was extracted, incubated with Micrococcus luteus uv-endonuclease and sedimented in alkaline sucrose. The number of endonuclease sensitive sites decreased as the time between uv irradiation and pulse-labeling of daughter DNA increased. Further, there were significantly less endonuclease sensitive sites in the daughter DNA from cells irradiated in the G 1 -phase than in the S-phase. These data indicate that very few, if any, dimers are transferred from parental DNA to daughter DNA and that the dimers detected in daughter DNA may be due to the irradiation of replicating daughter DNA before labeling

Specific action of T4 endonuclease V on damaged DNA in xeroderma pigmentosum cells in vivo

International Nuclear Information System (INIS)

Tanaka, K.; Hayakawa, H.; Sekiguchi, M.; Okada, Y.

1977-01-01

The specific action of T4 endonuclease V on damaged DNA in xeroderma pigmentosum cells was examined using an in vivo assay system with hemagglutinating virus of Japan (Sendai virus) inactivated by uv light. A clear dose response was observed between the level of uv-induced unscheduled DNA synthesis of xeroderma pigmentosum cells and the amount of T4 endonuclease V activity added. The T4 enzyme was unstable in human cells, and its half-life was 3 hr. Fractions derived from an extract of Escherichia coli infected with T4v 1 , a mutant defective in the endonuclease V gene, showed no ability to restore the uv-induced unscheduled DNA synthesis of xeroderma pigmentosum cells. However, fractions derived from an extract of T4D-infected E. coli with endonuclease V activity were effective. The T4 enzyme was effective in xeroderma pigmentosum cells on DNA damaged by uv light but not in cells damaged by 4-nitroquinoline 1-oxide. The results of these experiments show that the T4 enzyme has a specific action on human cell DNA in vivo. Treatment with the T4 enzyme increased the survival of group A xeroderma pigmentosum cells after uv irradiation

Molecular Recognition of DNA Damage Sites by Apurinic/Apyrimidinic Endonucleases

Energy Technology Data Exchange (ETDEWEB)

Braun, W. A.

2005-07-28

The DNA repair/redox factor AP endonuclease 1 (APE1) is a multifunctional protein which is known to to be essential for DNA repair activity in human cells. Structural/functional analyses of the APE activity is thus been an important research field to assess cellular defense mechanisms against ionizing radiation.

Recruitment of RecA homologs Dmc1p and Rad51p to the double-strand break repair site initiated by meiosis-specific endonuclease VDE (PI-SceI).

Science.gov (United States)

Fukuda, Tomoyuki; Ohya, Yoshikazu

2006-02-01

During meiosis, VDE (PI-SceI), a homing endonuclease in Saccharomyces cerevisiae, introduces a double-strand break (DSB) at its recognition sequence and induces homologous recombinational repair, called homing. Meiosis-specific RecA homolog Dmc1p, as well as mitotic RecA homolog Rad51p, acts in the process of meiotic recombination, being required for strand invasion and exchange. In this study, recruitment of Dmc1p and Rad51p to the VDE-induced DSB repair site is investigated by chromatin immunoprecipitation assay. It is revealed that Dmc1p and Rad51p are loaded to the repair site in an independent manner. Association of Rad51p requires other DSB repair proteins of Rad52p, Rad55p, and Rad57p, while loading of Dmc1p is facilitated by the different protein, Sae3p. Absence of Tid1p, which can bind both RecA homologs, appears specifically to cause an abnormal distribution of Dmc1p. Lack of Hop2, Mnd1p, and Sae1p does not impair recruitment of both RecA homologs. These findings reveal the discrete functions of each strand invasion protein in VDE-initiated homing, confirm the similarity between VDE-initiated homing and Spo11p-initiated meiotic recombination, and demonstrate the availability of VDE-initiated homing for the study of meiotic recombination.

Expression and Purification of BmrI Restriction Endonuclease and Its N-terminal Cleavage Domain Variants

OpenAIRE

Bao, Yongming; Higgins, Lauren; Zhang, Penghua; Chan, Siu-hong; Laget, Sophie; Sweeney, Suzanne; Lunnen, Keith; Xu, Shuang-yong

2007-01-01

BmrI (ACTGGG N5/N4) is one of the few metal-independent restriction endonucleases (REases) found in bacteria. The BmrI restriction-modification system was cloned by the methylase selection method, inverse PCR, and PCR. BmrI REase shows significant amino acid sequence identity to BfiI and a putative endonuclease MspBNCORF3798 from the sequenced Mesorhizobium sp. BNC1 genome. The EDTA-resistant BmrI REase was successfully over-expressed in a pre-modified E. coli strain from pET21a or pBAC-expIQ...

Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus.

Science.gov (United States)

Fukui, Kenji; Iino, Hitoshi; Baba, Seiki; Kumasaka, Takashi; Kuramitsu, Seiki; Yano, Takato

2017-09-01

DNA mismatch repair (MMR) system corrects mismatched bases that are generated mainly by DNA replication errors. The repair system excises the error-containing single-stranded region and enables the re-synthesis of the strand. In the early reactions of MMR, MutL endonuclease incises the newly-synthesized/error-containing strand of the duplex to initiate the downstream excision reaction. MutL endonuclease consists of the N-terminal ATPase and C-terminal endonuclease domains. In this study, we report the crystal structure of the ATPase domain of MutL endonuclease from Aquifex aeolicus. The overall structure of the domain was similar to those of human MutL homologs and Escherichia coli MutL, although E. coli MutL has no endonuclease activity. The ATPase domain was comprised of two subdomains: the N-terminal ATP-binding subdomain and the C-terminal α-β sandwich subdomain. Site-directed mutagenesis experiment identified DNA-interacting eight basic amino acid residues, which were distributed across both the two subdomains and formed a DNA-binding cleft. Docking simulation between the structures of the ATPase and endonuclease domains generated a reliable model structure for the full-length A. aeolicus MutL, which satisfies our previous result of small-angle X-ray scattering analysis. On the basis of the model structure and further experimental results, we concluded that the two separate DNA-binding sites in the full-length A. aeolicus MutL simultaneously bind a dsDNA molecule. Copyright © 2017 Elsevier B.V. All rights reserved.

Measurement of M. luteus endonuclease-sensitive lesions by alkaline elution

Energy Technology Data Exchange (ETDEWEB)

Fornace, Jr, A J [National Cancer Inst., Bethesda, MD (USA). Lab. for Experimental Pathology

1982-01-01

The UV-endonuclease approach to detect DNA damage has been combined with the alkaline elution technique with a resultant marked increase in sensitivity compared to the conventional method using alkaline sedimentation. DNA from UV-irradiated cells was digested on an inert filter with an extract from Micrococcus luteus and then analyzed by alkaline elution. Endonuclease-sensitive sites (endo-sites) were measured after doses of 0.08-0.7 Jm/sup -2/ of UV-radiation. An estimate of endo-site production with UV radiation, 0.27 endo-sites/10/sup 8/ daltons of DNA/0.1 Jm/sup -2/, was similar to that usually seen at higher doses by others. With repair incubation, approx. 50% of the endo-sites were removed in 4 h by normal human fibroblasts after 0.2 or 0.4 Jm/sup -2/, no appreciable repair was seen in xeroderma pigmentosum fibroblasts from complementation group A after 24 h of repair incubation. No photoreaction of UV damage due to 0.4 Jm/sup -2/ was detected in normal human fibroblasts.

Measurement of M. luteus endonuclease-sensitive lesions by alkaline elution

International Nuclear Information System (INIS)

Fornace, A.J. Jr.

1982-01-01

The UV-endonuclease approach to detect DNA damage has been combined with the alkaline elution technique with a resultant marked increase in sensitivity compared to the conventional method using alkaline sedimentation. DNA from UV-irradiated cells was digested on an inert filter with an extract from Micrococcus luteus and then analyzed by alkaline elution. Endonuclease-sensitive sites (endo-sites) were measured after doses of 0.08-0.7 Jm -2 of UV-radiation. An estimate of endo-site production with UV radiation, 0.27 endo-sites/10 8 daltons of DNA/0.1 Jm -2 , was similar to that usually seen at higher doses by others. With repair incubation, approx. 50% of the endo-sites were removed in 4 h by normal human fibroblasts after 0.2 or 0.4 Jm -2 , no appreciable repair was seen in xeroderma pigmentosum fibroblasts from complementation group A after 24 h of repair incubation. No photoreaction of UV damage due to 0.4 Jm -2 was detected in normal human fibroblasts. (orig./AJ)

The mitochondrial LSU rRNA group II intron of Ustilago maydis encodes an active homing endonuclease likely involved in intron mobility.

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Anja Pfeifer

Full Text Available BACKGROUND: The a2 mating type locus gene lga2 is critical for uniparental mitochondrial DNA inheritance during sexual development of Ustilago maydis. Specifically, the absence of lga2 results in biparental inheritance, along with efficient transfer of intronic regions in the large subunit rRNA gene between parental molecules. However, the underlying role of the predicted LAGLIDADG homing endonuclease gene I-UmaI located within the group II intron LRII1 has remained unresolved. METHODOLOGY/PRINCIPAL FINDINGS: We have investigated the enzymatic activity of I-UmaI in vitro based on expression of a tagged full-length and a naturally occurring mutant derivative, which harbors only the N-terminal LAGLIDADG domain. This confirmed Mg²⁺-dependent endonuclease activity and cleavage at the LRII1 insertion site to generate four base pair extensions with 3' overhangs. Specifically, I-UmaI recognizes an asymmetric DNA sequence with a minimum length of 14 base pairs (5'-GACGGGAAGACCCT-3' and tolerates subtle base pair substitutions within the homing site. Enzymatic analysis of the mutant variant indicated a correlation between the activity in vitro and intron homing. Bioinformatic analyses revealed that putatively functional or former functional I-UmaI homologs are confined to a few members within the Ustilaginales and Agaricales, including the phylogenetically distant species Lentinula edodes, and are linked to group II introns inserted into homologous positions in the LSU rDNA. CONCLUSIONS/SIGNIFICANCE: The present data provide strong evidence that intron homing efficiently operates under conditions of biparental inheritance in U. maydis. Conversely, uniparental inheritance may be critical to restrict the transmission of mobile introns. Bioinformatic analyses suggest that I-UmaI-associated introns have been acquired independently in distant taxa and are more widespread than anticipated from available genomic data.

Variable angle asymmetric cut monochromator

International Nuclear Information System (INIS)

Smither, R.K.; Fernandez, P.B.

1993-09-01

A variable incident angle, asymmetric cut, double crystal monochromator was tested for use on beamlines at the Advanced Photon Source (APS). For both undulator and wiggler beams the monochromator can expand area of footprint of beam on surface of the crystals to 50 times the area of incident beam; this will reduce the slope errors by a factor of 2500. The asymmetric cut allows one to increase the acceptance angle for incident radiation and obtain a better match to the opening angle of the incident beam. This can increase intensity of the diffracted beam by a factor of 2 to 5 and can make the beam more monochromatic, as well. The monochromator consists of two matched, asymmetric cut (18 degrees), silicon crystals mounted so that they can be rotated about three independent axes. Rotation around the first axis controls the Bragg angle. The second rotation axis is perpendicular to the diffraction planes and controls the increase of the area of the footprint of the beam on the crystal surface. Rotation around the third axis controls the angle between the surface of the crystal and the wider, horizontal axis for the beam and can make the footprint a rectangle with a minimum. length for this area. The asymmetric cut is 18 degrees for the matched pair of crystals, which allows one to expand the footprint area by a factor of 50 for Bragg angles up to 19.15 degrees (6 keV for Si[111] planes). This monochromator, with proper cooling, will be useful for analyzing the high intensity x-ray beams produced by both undulators and wigglers at the APS

Inroads into base excision repair I. The discovery of apurinic/apyrimidinic (AP) endonuclease. "An endonuclease for depurinated DNA in Escherichia coli B," Canadian Journal of Biochemistry, 1972.

Science.gov (United States)

Lindahl, Tomas; Verly, W G; Paquette Y

2004-11-02

DNA treated with alkylating agents is incised at sites of damage by cell extracts. A key component of this DNA repair function was shown by Verly and co-workers to be an endonuclease acting at secondary lesions, apurinic sites, rather than directly at alkylated nucleotide residues.

Enhancement of ultraviolet-DNA repair in denV gene transfectants and T4 endonuclease V-liposome recipients

International Nuclear Information System (INIS)

Kibitel, J.T.; Yee, V.; Yarosh, D.B.

1991-01-01

The phage T4 denV gene, coding for the pyrimidine-dimer specific T4 endonuclease V, was transfected into human repair-proficient fibroblasts, repair-deficient xeroderma pigmentosum fibroblasts, and wild type CHO hamster cells. Transfectants maintained denV DNA and expressed denV mRNA. Purified T4 endonuclease V encapsulated in liposomes was also used to treat repair-proficient and -deficient human cells. The denV transfected clones and liposome-treated cells showed increased unscheduled DNA synthesis and enhanced removal of pyrimidine dimers compared to controls. Both denV gene transfection and endonuclease V liposome treatment enhanced post-UV survival in xeroderma pigmentosum cells but had no effect on survival in repair-proficient human or hamster cells. The results demonstrate that an exogenous DNA repair enzyme can correct the DNA repair defect in xeroderma pigmentosum cells and enhance DNA repair in normal cells. (author)

Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease.

Science.gov (United States)

Anders, Carolin; Niewoehner, Ole; Duerst, Alessia; Jinek, Martin

2014-09-25

The CRISPR-associated protein Cas9 is an RNA-guided endonuclease that cleaves double-stranded DNA bearing sequences complementary to a 20-nucleotide segment in the guide RNA. Cas9 has emerged as a versatile molecular tool for genome editing and gene expression control. RNA-guided DNA recognition and cleavage strictly require the presence of a protospacer adjacent motif (PAM) in the target DNA. Here we report a crystal structure of Streptococcus pyogenes Cas9 in complex with a single-molecule guide RNA and a target DNA containing a canonical 5'-NGG-3' PAM. The structure reveals that the PAM motif resides in a base-paired DNA duplex. The non-complementary strand GG dinucleotide is read out via major-groove interactions with conserved arginine residues from the carboxy-terminal domain of Cas9. Interactions with the minor groove of the PAM duplex and the phosphodiester group at the +1 position in the target DNA strand contribute to local strand separation immediately upstream of the PAM. These observations suggest a mechanism for PAM-dependent target DNA melting and RNA-DNA hybrid formation. Furthermore, this study establishes a framework for the rational engineering of Cas9 enzymes with novel PAM specificities.

Atomic Structure and Biochemical Characterization of an RNA Endonuclease in the N Terminus of Andes Virus L Protein.

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Yaiza Fernández-García

2016-06-01

Full Text Available Andes virus (ANDV is a human-pathogenic hantavirus. Hantaviruses presumably initiate their mRNA synthesis by using cap structures derived from host cell mRNAs, a mechanism called cap-snatching. A signature for a cap-snatching endonuclease is present in the N terminus of hantavirus L proteins. In this study, we aimed to solve the atomic structure of the ANDV endonuclease and characterize its biochemical features. However, the wild-type protein was refractory to expression in Escherichia coli, presumably due to toxic enzyme activity. To circumvent this problem, we introduced attenuating mutations in the domain that were previously shown to enhance L protein expression in mammalian cells. Using this approach, 13 mutant proteins encompassing ANDV L protein residues 1-200 were successfully expressed and purified. Protein stability and nuclease activity of the mutants was analyzed and the crystal structure of one mutant was solved to a resolution of 2.4 Å. Shape in solution was determined by small angle X-ray scattering. The ANDV endonuclease showed structural similarities to related enzymes of orthobunya-, arena-, and orthomyxoviruses, but also differences such as elongated shape and positively charged patches surrounding the active site. The enzyme was dependent on manganese, which is bound to the active site, most efficiently cleaved single-stranded RNA substrates, did not cleave DNA, and could be inhibited by known endonuclease inhibitors. The atomic structure in conjunction with stability and activity data for the 13 mutant enzymes facilitated inference of structure-function relationships in the protein. In conclusion, we solved the structure of a hantavirus cap-snatching endonuclease, elucidated its catalytic properties, and present a highly active mutant form, which allows for inhibitor screening.

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

Energy Technology Data Exchange (ETDEWEB)

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

2010-03-01

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

Cofactor requirement of HpyAV restriction endonuclease.

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Siu-Hong Chan

Full Text Available BACKGROUND: Helicobacter pylori is the etiologic agent of common gastritis and a risk factor for gastric cancer. It is also one of the richest sources of Type II restriction-modification (R-M systems in microorganisms. PRINCIPAL FINDINGS: We have cloned, expressed and purified a new restriction endonuclease HpyAV from H. pylori strain 26695. We determined the HpyAV DNA recognition sequence and cleavage site as CCTTC 6/5. In addition, we found that HpyAV has a unique metal ion requirement: its cleavage activity is higher with transition metal ions than in Mg(++. The special metal ion requirement of HpyAV can be attributed to the presence of a HNH catalytic site similar to ColE9 nuclease instead of the canonical PD-X-D/EXK catalytic site found in many other REases. Site-directed mutagenesis was carried out to verify the catalytic residues of HpyAV. Mutation of the conserved metal-binding Asn311 and His320 to alanine eliminated cleavage activity. HpyAV variant H295A displayed approximately 1% of wt activity. CONCLUSIONS/SIGNIFICANCE: Some HNH-type endonucleases have unique metal ion cofactor requirement for optimal activities. Homology modeling and site-directed mutagenesis confirmed that HpyAV is a member of the HNH nuclease family. The identification of catalytic residues in HpyAV paved the way for further engineering of the metal binding site. A survey of sequenced microbial genomes uncovered 10 putative R-M systems that show high sequence similarity to the HpyAV system, suggesting lateral transfer of a prototypic HpyAV-like R-M system among these microorganisms.

Crystallographic and Modeling Studies of RNase III Suggest a Mechanism for Double-Stranded RNA Cleavage | Center for Cancer Research

Science.gov (United States)

Background: Ribonuclease III belongs to the family of Mg2+-dependent endonucleases that show specificity for double-stranded RNA (dsRNA). RNase III is conserved in all known bacteria and eukaryotes and has 1–2 copies of a 9-residue consensus sequence, known as the RNase III signature motif. The bacterial RNase III proteins are the simplest, consisting of two domains: an

Modelling of parameters for asymmetric halo and symmetric DHDMG n-MOSFETs

Science.gov (United States)

De, Swapnadip; Sarkar, Angsuman; Sarkar, Chandan Kumar

2011-10-01

This article presents an analytical surface potential, threshold voltage and drain current model for asymmetric pocket-implanted, single-halo dual material gate and double-halo dual material gate (DHDMG) n-MOSFET (MOSFET, metal-oxide-semiconductor field-effect transistor) operating up to 40 nm regime. The model is derived by applying Gauss's law to a rectangular box, covering the entire depletion region. The asymmetric pocket-implanted model takes into account the effective doping concentration of the two linear pocket profiles at the source and the drain ends along with the inner fringing capacitances at both the source and the drain ends and the subthreshold drain and the substrate bias effect. Using the surface potential model, the threshold voltage and drain currents are estimated. The same model is used to find the characteristic parameters for dual-material gate (DMG) with halo implantations and double gate. The characteristic improvement is investigated. It is concluded that the DHDMG device structure exhibits better suppression of the short-channel effect (SCE) and the threshold voltage roll-off than DMG and double-gate MOSFET. The adequacy of the model is verified by comparing with two-dimensional device simulator DESSIS. A very good agreement of our model with DESSIS is obtained proving the validity of our model used in suppressing the SCEs.

Symmetric vs. asymmetric stem cell divisions: an adaptation against cancer?

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Leili Shahriyari

Full Text Available Traditionally, it has been held that a central characteristic of stem cells is their ability to divide asymmetrically. Recent advances in inducible genetic labeling provided ample evidence that symmetric stem cell divisions play an important role in adult mammalian homeostasis. It is well understood that the two types of cell divisions differ in terms of the stem cells' flexibility to expand when needed. On the contrary, the implications of symmetric and asymmetric divisions for mutation accumulation are still poorly understood. In this paper we study a stochastic model of a renewing tissue, and address the optimization problem of tissue architecture in the context of mutant production. Specifically, we study the process of tumor suppressor gene inactivation which usually takes place as a consequence of two "hits", and which is one of the most common patterns in carcinogenesis. We compare and contrast symmetric and asymmetric (and mixed stem cell divisions, and focus on the rate at which double-hit mutants are generated. It turns out that symmetrically-dividing cells generate such mutants at a rate which is significantly lower than that of asymmetrically-dividing cells. This result holds whether single-hit (intermediate mutants are disadvantageous, neutral, or advantageous. It is also independent on whether the carcinogenic double-hit mutants are produced only among the stem cells or also among more specialized cells. We argue that symmetric stem cell divisions in mammals could be an adaptation which helps delay the onset of cancers. We further investigate the question of the optimal fraction of stem cells in the tissue, and quantify the contribution of non-stem cells in mutant production. Our work provides a hypothesis to explain the observation that in mammalian cells, symmetric patterns of stem cell division seem to be very common.

Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication.

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Eveline Kindler

2017-02-01

Full Text Available Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I. This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU activity is key to prevent early induction of double-stranded RNA (dsRNA host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis-within the replicase complex-suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses.

Creating a monomeric endonuclease TALE-I-SceI with high specificity and low genotoxicity in human cells.

Science.gov (United States)

Lin, Jianfei; Chen, He; Luo, Ling; Lai, Yongrong; Xie, Wei; Kee, Kehkooi

2015-01-01

To correct a DNA mutation in the human genome for gene therapy, homology-directed repair (HDR) needs to be specific and have the lowest off-target effects to protect the human genome from deleterious mutations. Zinc finger nucleases, transcription activator-like effector nuclease (TALEN) and CRISPR-CAS9 systems have been engineered and used extensively to recognize and modify specific DNA sequences. Although TALEN and CRISPR/CAS9 could induce high levels of HDR in human cells, their genotoxicity was significantly higher. Here, we report the creation of a monomeric endonuclease that can recognize at least 33 bp by fusing the DNA-recognizing domain of TALEN (TALE) to a re-engineered homing endonuclease I-SceI. After sequentially re-engineering I-SceI to recognize 18 bp of the human β-globin sequence, the re-engineered I-SceI induced HDR in human cells. When the re-engineered I-SceI was fused to TALE (TALE-ISVB2), the chimeric endonuclease induced the same HDR rate at the human β-globin gene locus as that induced by TALEN, but significantly reduced genotoxicity. We further demonstrated that TALE-ISVB2 specifically targeted at the β-globin sequence in human hematopoietic stem cells. Therefore, this monomeric endonuclease has the potential to be used in therapeutic gene targeting in human cells. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cleavage and protection of locked nucleic acid-modified DNA by restriction endonucleases

DEFF Research Database (Denmark)

Crouzier, Lucile; Dubois, Camille; Wengel, Jesper

2012-01-01

Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far. We herein for the first time report cleavage by restriction endonuclease of LNA-modified DNA oligonucleotides. The experiments revealed that RsaI is an efficient enzyme capable of recognizing and cleaving...

Axisymmetric stability of vertically asymmetric Tokamaks at large beta poloidal

Energy Technology Data Exchange (ETDEWEB)

Yamazaki, K.; Fishman, H.; Okabayashi, M. (Princeton Univ., NJ (USA). Plasma Physics Lab.); Todd, A.M.M. (Grumman Aerospace Corp., Princeton, NJ (USA))

1983-11-01

The rigid-mode stability of high-..beta.. vertically asymmetric Tokamak equilibria with quasi-uniform current profile is investigated analytically using toroidicity-shaping double expansion method. It is found that vertical stability at large beta poloidal is mainly determined by a coupling between the shape of the plasma surface and the Shafranov shift of the magnetic axis. To the lowest order, symmetric components of the plasma surface shape are found to be the critical destabilizing elements. Asymmetric components have little effect. The inclusion of higher order terms in the high-..beta.. Tokamak expansion leads to further destabilization. These analytic insights are qualitatively confirmed by numerical stability calculations using the PEST code with parabolic safety-factor profile.

Low frequency noise in asymmetric double barrier magnetic tunnel junctions with a top thin MgO layer

International Nuclear Information System (INIS)

Guo Hui-Qiang; Tang Wei-Yue; Liu Liang; Wei Jian; Li Da-Lai; Feng Jia-Feng; Han Xiu-Feng

2015-01-01

Low frequency noise has been investigated at room temperature for asymmetric double barrier magnetic tunnel junctions (DBMTJs), where the coupling between the top and middle CoFeB layers is antiferromagnetic with a 0.8-nm thin top MgO barrier of the CoFeB/MgO/CoFe/CoFeB/MgO/CoFeB DBMTJ. At enough large bias, 1/f noise dominates the voltage noise power spectra in the low frequency region, and is conventionally characterized by the Hooge parameter α mag . With increasing external field, the top and bottom ferromagnetic layers are aligned by the field, and then the middle free layer rotates from antiparallel state (antiferromagnetic coupling between top and middle ferromagnetic layers) to parallel state. In this rotation process α mag and magnetoresistance-sensitivity-product show a linear dependence, consistent with the fluctuation dissipation relation. With the magnetic field applied at different angles (θ) to the easy axis of the free layer, the linear dependence persists while the intercept of the linear fit satisfies a cos(θ) dependence, similar to that for the magnetoresistance, suggesting intrinsic relation between magnetic losses and magnetoresistance. (rapid communication)

Small molecule inhibitors uncover synthetic genetic interactions of human flap endonuclease 1 (FEN1 with DNA damage response genes.

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Thomas A Ward

Full Text Available Flap endonuclease 1 (FEN1 is a structure selective endonuclease required for proficient DNA replication and the repair of DNA damage. Cellularly active inhibitors of this enzyme have previously been shown to induce a DNA damage response and, ultimately, cell death. High-throughput screens of human cancer cell-lines identify colorectal and gastric cell-lines with microsatellite instability (MSI as enriched for cellular sensitivity to N-hydroxyurea series inhibitors of FEN1, but not the PARP inhibitor olaparib or other inhibitors of the DNA damage response. This sensitivity is due to a synthetic lethal interaction between FEN1 and MRE11A, which is often mutated in MSI cancers through instabilities at a poly(T microsatellite repeat. Disruption of ATM is similarly synthetic lethal with FEN1 inhibition, suggesting that disruption of FEN1 function leads to the accumulation of DNA double-strand breaks. These are likely a result of the accumulation of aberrant replication forks, that accumulate as a consequence of a failure in Okazaki fragment maturation, as inhibition of FEN1 is toxic in cells disrupted for the Fanconi anemia pathway and post-replication repair. Furthermore, RAD51 foci accumulate as a consequence of FEN1 inhibition and the toxicity of FEN1 inhibitors increases in cells disrupted for the homologous recombination pathway, suggesting a role for homologous recombination in the resolution of damage induced by FEN1 inhibition. Finally, FEN1 appears to be required for the repair of damage induced by olaparib and cisplatin within the Fanconi anemia pathway, and may play a role in the repair of damage associated with its own disruption.

Cell-Autonomous Progeroid Changes in Conditional Mouse Models for Repair Endonuclease XPG Deficiency

NARCIS (Netherlands)

S. Barnhoorn (Sander); L.M. Uittenboogaard (Lieneke); D. Jaarsma (Dick); W.P. Vermeij (Wilbert); M. Tresini (Maria); M. Weymaere (Michael); H. Menoni (Hervé); R.M.C. Brandt (Renata); M.C. de Waard (Monique); S.M. Botter (Sander); A.H. Sarker (Altraf); N.G.J. Jaspers (Nicolaas); G.T.J. van der Horst (Gijsbertus); P.K. Cooper (Priscilla K.); J.H.J. Hoeijmakers (Jan); I. van der Pluijm (Ingrid)

2014-01-01

textabstractAs part of the Nucleotide Excision Repair (NER) process, the endonuclease XPG is involved in repair of helix-distorting DNA lesions, but the protein has also been implicated in several other DNA repair systems, complicating genotype-phenotype relationship in XPG patients. Defects in XPG

A mean-field theory on the differential capacitance of asymmetric ionic liquid electrolytes.

Science.gov (United States)

Han, Yining; Huang, Shanghui; Yan, Tianying

2014-07-16

The size of ions significantly influences the electric double layer structure of room temperature ionic liquid (IL) electrolytes and their differential capacitance (Cd). In this study, we extended the mean-field theory (MFT) developed independently by Kornyshev (2007J. Phys. Chem. B 111 5545-57) and Kilic, Bazant, and Ajdari (2007 Phys. Rev. E 75 021502) (the KKBA MFT) to take into account the asymmetric 1:1 IL electrolytes by introducing an additional parameter ξ for the anion/cation volume ratio, besides the ionic compressibility γ in the KKBA MFT. The MFT of asymmetric ions becomes KKBA MFT upon ξ = 1, and further reduces to Gouy-Chapman theory in the γ → 0 limit. The result of the extended MFT demonstrates that the asymmetric ILs give rise to an asymmetric Cd, with the higher peak in Cd occurring at positive polarization for the smaller anionic size. At high potential, Cd decays asymptotically toward KKBA MFT characterized by γ for the negative polarization, and characterized by ξγ for the positive polarization, with inverse-square-root behavior. At low potential, around the potential of zero charge, the asymmetric ions cause a higher Cd, which exceeds that of Gouy-Chapman theory.

An analysis of the repair processes in ultraviolet-irradiated Micrococcus luteus using purified ultraviolet-endonuclease

International Nuclear Information System (INIS)

Tomilin, N.V.; Zherebtsov, S.V.

1982-01-01

The measurement of the frequency of endonucleolytic incisions in ultraviolet-irradiated DNA serves as the test for the presence of pyrimidine dimers. In accordance with this approach, the lysates of three Micrococcus luteus strains containing radioactively labeled chromosomes were treated with purified M. luteus ultraviolet-endonuclease to trace segregation of dimers amongst parental and newly synthesized DNA and their removal during postreplication and excision DNA repair. A considerable proportion of the dimers in all strains tested proved to be insensitive to the action of exogenous incising enzyme. The use of chloramphenicol as an inhibitor of postirradiation protein synthesis in combination with ultraviolet-endonuclease treatment of DNA allowed to reveal at least two alternative pathways of postreplication repair: constitutively active recombinational pathway and inducible nonrecombinational one. (Auth.)

A detailed experimental study of a DNA computer with two endonucleases.

Science.gov (United States)

Sakowski, Sebastian; Krasiński, Tadeusz; Sarnik, Joanna; Blasiak, Janusz; Waldmajer, Jacek; Poplawski, Tomasz

2017-07-14

Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effect of the number of states, the length of input data, and the nondeterminism on the computing process. We also tested different automata (with three, four, and six states) running on various accepted input words of different lengths such as ab, aab, aaab, ababa, and of an unaccepted word ba. Moreover, this article presents the reaction optimization and the methods of eliminating certain biochemical problems occurring in the implementation of a biomolecular DNA automaton based on two endonucleases.

Shifted one-parameter supersymmetric family of quartic asymmetric double-well potentials

International Nuclear Information System (INIS)

Rosu, Haret C.; Mancas, Stefan C.; Chen, Pisin

2014-01-01

Extending our previous work (Rosu, 2014), we define supersymmetric partner potentials through a particular Riccati solution of the form F(x)=(x−c) 2 −1, where c is a real shift parameter, and work out the quartic double-well family of one-parameter isospectral potentials obtained by using the corresponding general Riccati solution. For these parametric double well potentials, we study how the localization properties of the two wells depend on the parameter of the potentials for various values of the shifting parameter. We also consider the supersymmetric parametric family of the first double-well potential in the Razavy chain of double well potentials corresponding to F(x)=1/2 sinh2x−2((1+√(2))sinh2x)/((1+√(2))cosh2x+1) , both unshifted and shifted, to test and compare the localization properties. - Highlights: • Quartic one-parameter DWs with an additional shift parameter are introduced. • Anomalous localization feature of their zero modes is confirmed at different shifts. • Razavy one-parameter DWs are also introduced and shown not to have this feature

Shifted one-parameter supersymmetric family of quartic asymmetric double-well potentials

Energy Technology Data Exchange (ETDEWEB)

Rosu, Haret C., E-mail: hcr@ipicyt.edu.mx [IPICYT, Instituto Potosino de Investigacion Cientifica y Tecnologica, Camino a la presa San José 2055, Col. Lomas 4a Sección, 78216 San Luis Potosí, S.L.P. (Mexico); Mancas, Stefan C., E-mail: mancass@erau.edu [Department of Mathematics, Embry-Riddle Aeronautical University, Daytona Beach, FL 32114-3900 (United States); Chen, Pisin, E-mail: pisinchen@phys.ntu.edu.tw [Leung Center for Cosmology and Particle Astrophysics (LeCosPA) and Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China)

2014-10-15

Extending our previous work (Rosu, 2014), we define supersymmetric partner potentials through a particular Riccati solution of the form F(x)=(x−c){sup 2}−1, where c is a real shift parameter, and work out the quartic double-well family of one-parameter isospectral potentials obtained by using the corresponding general Riccati solution. For these parametric double well potentials, we study how the localization properties of the two wells depend on the parameter of the potentials for various values of the shifting parameter. We also consider the supersymmetric parametric family of the first double-well potential in the Razavy chain of double well potentials corresponding to F(x)=1/2 sinh2x−2((1+√(2))sinh2x)/((1+√(2))cosh2x+1) , both unshifted and shifted, to test and compare the localization properties. - Highlights: • Quartic one-parameter DWs with an additional shift parameter are introduced. • Anomalous localization feature of their zero modes is confirmed at different shifts. • Razavy one-parameter DWs are also introduced and shown not to have this feature.

Strategy for improved frequency response of electric double-layer capacitors

Science.gov (United States)

Wada, Yoshifumi; Pu, Jiang; Takenobu, Taishi

2015-10-01

We propose a strategy for improving the response speed of electric double-layer capacitors (EDLCs) and electric double-layer transistors (EDLTs), based on an asymmetric structure with differently sized active materials and gate electrodes. We validate the strategy analytically by a classical calculation and experimentally by fabricating EDLCs with asymmetric Au electrodes (1:50 area ratio and 7.5 μm gap distance). The performance of the EDLCs is compared with that of conventional symmetric EDLCs. Our strategy dramatically improved the cut-off frequency from 14 to 93 kHz and this improvement is explained by fast charging of smaller electrodes. Therefore, this approach is particularly suitable to EDLTs, potentially expanding the applicability to medium speed (kHz-MHz) devices.

Asymmetric-cut variable-incident-angle monochromator.

Science.gov (United States)

Smither, R K; Graber, T J; Fernandez, P B; Mills, D M

2012-03-01

A novel asymmetric-cut variable-incident-angle monochromator was constructed and tested in 1997 at the Advanced Photon Source of Argonne National Laboratory. The monochromator was originally designed as a high heat load monochromator capable of handling 5-10 kW beams from a wiggler source. This was accomplished by spreading the x-ray beam out on the surface an asymmetric-cut crystal and by using liquid metal cooling of the first crystal. The monochromator turned out to be a highly versatile monochromator that could perform many different types of experiments. The monochromator consisted of two 18° asymmetrically cut Si crystals that could be rotated about 3 independent axes. The first stage (Φ) rotates the crystal around an axis perpendicular to the diffraction plane. This rotation changes the angle of the incident beam with the surface of the crystal without changing the Bragg angle. The second rotation (Ψ) is perpendicular to the first and is used to control the shape of the beam footprint on the crystal. The third rotation (Θ) controls the Bragg angle. Besides the high heat load application, the use of asymmetrically cut crystals allows one to increase or decrease the acceptance angle for crystal diffraction of a monochromatic x-ray beam and allows one to increase or decrease the wavelength bandwidth of the diffraction of a continuum source like a bending-magnet beam or a normal x-ray-tube source. When the monochromator is used in the doubly expanding mode, it is possible to expand the vertical size of the double-diffracted beam by a factor of 10-15. When this was combined with a bending magnet source, it was possible to generate an 8 keV area beam, 16 mm wide by 26 mm high with a uniform intensity and parallel to 1.2 arc sec that could be applied in imaging experiments.

Thermogravimetric pyrolysis kinetics of bamboo waste via Asymmetric Double Sigmoidal (Asym2sig) function deconvolution.

Science.gov (United States)

Chen, Chuihan; Miao, Wei; Zhou, Cheng; Wu, Hongjuan

2017-02-01

Thermogravimetric kinetic of bamboo waste (BW) pyrolysis has been studied using Asymmetric Double Sigmoidal (Asym2sig) function deconvolution. Through deconvolution, BW pyrolytic profiles could be separated into three reactions well, each of which corresponded to pseudo hemicelluloses (P-HC), pseudo cellulose (P-CL), and pseudo lignin (P-LG) decomposition. Based on Friedman method, apparent activation energy of P-HC, P-CL, P-LG was found to be 175.6kJ/mol, 199.7kJ/mol, and 158.4kJ/mol, respectively. Energy compensation effects (lnk 0, z vs. E z ) of pseudo components were in well linearity, from which pre-exponential factors (k 0 ) were determined as 6.22E+11s -1 (P-HC), 4.50E+14s -1 (P-CL) and 1.3E+10s -1 (P-LG). Integral master-plots results showed pyrolytic mechanism of P-HC, P-CL, and P-LG was reaction order of f(α)=(1-α) 2 , f(α)=1-α and f(α)=(1-α) n (n=6-8), respectively. Mechanism of P-HC and P-CL could be further reconstructed to n-th order Avrami-Erofeyev model of f(α)=0.62(1-α)[-ln(1-α)] -0.61 (n=0.62) and f(α)=1.08(1-α)[-ln(1-α)] 0.074 (n=1.08). Two-steps reaction was more suitable for P-LG pyrolysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function

Czech Academy of Sciences Publication Activity Database

McDermott-Roe, Ch.; Ye, J.; Ahmed, R.; Sun, X. M.; Serafín, A.; Ware, J.; Bottolo, L.; Muckett, P.; Caňas, X.; Zhang, J.; Rowe, G. C.; Buchan, R.; Lu, H.; Braithwaite, A.; Mancini, M.; Hauton, D.; Martí, R.; García-Arumí, E.; Hubner, N.; Jacob, H.; Serikawa, T.; Zídek, Václav; Papoušek, František; Kolář, František; Cardona, M.; Ruiz-Meana, M.; García-Dorado, D.; Comella, J. X.; Felkin, L. E.; Barton, P. J. R.; Arany, Z.; Pravenec, Michal; Petretto, E.; Sanchis, D.; Cook, S.A.

2011-01-01

Roč. 478, č. 7367 (2011), s. 114-118 ISSN 0028-0836 R&D Projects: GA MŠk(CZ) 1M0520; GA ČR(CZ) GA301/08/0166 Institutional research plan: CEZ:AV0Z50110509 Keywords : left ventricular hypertrophy * endonuclease G * mitochondrial dysfunction Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 36.280, year: 2011

Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases

Czech Academy of Sciences Publication Activity Database

Kielkowski, Pavel; Macíčková-Cahová, Hana; Pohl, Radek; Hocek, Michal

2011-01-01

Roč. 50, č. 37 (2011), s. 8727-8730 ISSN 1433-7851 R&D Projects: GA ČR GA203/09/0317 Institutional research plan: CEZ:AV0Z40550506 Keywords : alkynes * DNA * protecting groups * nucleotides * restriction endonucleases Subject RIV: CC - Organic Chemistry Impact factor: 13.455, year: 2011

Asymmetric Synthesis of Potential Precursors of the HIV Drug MC1220 and Its Analogues by Hydrogenation of (1-Arylvinyl)pyrimidines

DEFF Research Database (Denmark)

Loksha, Yasser M.; Pedersen, Erik B.

2018-01-01

Because MC1220 is a promising microbicide with anti-HIV-1 activity, the possibility for asymmetric synthesis of its potential precursors is explored. Here, we investigate asymmetric reduction of the vinyl double bond of 6-(1-arylvinyl)pyrimidine derivatives to their corresponding ethylidene analo...... analogues. Catalysts with ligands bearing trivalent phosphorus ligating the soft metals rhodium(I), ruthenium(II), or iridium(I) are used for asymmetric reduction of the vinyl derivatives 5a-e. The enantioselective reduction reaches 92% ee and about 71% conversion for reduction of the 6...

Human RECQL5beta stimulates flap endonuclease 1

DEFF Research Database (Denmark)

Speina, Elzbieta; Dawut, Lale; Hedayati, Mohammad

2010-01-01

devoid of RECQL1 and RECQL5 display increased chromosomal instability. Here, we report the physical and functional interaction of the large isomer of RECQL5, RECQL5beta, with the human flap endonuclease 1, FEN1, which plays a critical role in DNA replication, recombination and repair. RECQL5beta...... dramatically stimulates the rate of FEN1 cleavage of flap DNA substrates. Moreover, we show that RECQL5beta and FEN1 interact physically and co-localize in the nucleus in response to DNA damage. Our findings, together with the previous literature on WRN, BLM and RECQL4's stimulation of FEN1, suggests...

Modeling and characterization of double resonant tunneling diodes for application as energy selective contacts in hot carrier solar cells

Science.gov (United States)

Jehl, Zacharie; Suchet, Daniel; Julian, Anatole; Bernard, Cyril; Miyashita, Naoya; Gibelli, Francois; Okada, Yoshitaka; Guillemolles, Jean-Francois

2017-02-01

Double resonant tunneling barriers are considered for an application as energy selective contacts in hot carrier solar cells. Experimental symmetric and asymmetric double resonant tunneling barriers are realized by molecular beam epitaxy and characterized by temperature dependent current-voltage measurements. The negative differential resistance signal is enhanced for asymmetric heterostructures, and remains unchanged between low- and room-temperatures. Within Tsu-Esaki description of the tunnel current, this observation can be explained by the voltage dependence of the tunnel transmission amplitude, which presents a resonance under finite bias for asymmetric structures. This effect is notably discussed with respect to series resistance. Different parameters related to the electronic transmission of the structure and the influence of these parameters on the current voltage characteristic are investigated, bringing insights on critical processes to optimize in double resonant tunneling barriers applied to hot carrier solar cells.

Biological significance of facilitated diffusion in protein-DNA interactions. Applications to T4 endonuclease V-initiated DNA repair

International Nuclear Information System (INIS)

Dowd, D.R.; Lloyd, R.S.

1990-01-01

Facilitated diffusion along nontarget DNA is employed by numerous DNA-interactive proteins to locate specific targets. Until now, the biological significance of DNA scanning has remained elusive. T4 endonuclease V is a DNA repair enzyme which scans nontarget DNA and processively incises DNA at the site of pyrimidine dimers which are produced by exposure to ultraviolet (UV) light. In this study we tested the hypothesis that there exists a direct correlation between the degree of processivity of wild type and mutant endonuclease V molecules and the degree of enhanced UV resistance which is conferred to repair-deficient Eshcerichia coli. This was accomplished by first creating a series of endonuclease V mutants whose in vitro catalytic activities were shown to be very similar to that of the wild type enzyme. However, when the mechanisms by which these enzymes search nontarget DNA for its substrate were analyzed in vitro and in vivo, the mutants displayed varying degrees of nontarget DNA scanning ranging from being nearly as processive as wild type to randomly incising dimers within the DNA population. The ability of these altered endonuclease V molecules to enhance UV survival in DNA repair-deficient E. coli then was assessed. The degree of enhanced UV survival was directly correlated with the level of facilitated diffusion. This is the first conclusive evidence directly relating a reduction of in vivo facilitated diffusion with a change in an observed phenotype. These results support the assertion that the mechanisms which DNA-interactive proteins employ in locating their target sites are of biological significance

Homing endonuclease genes: the rise and fall and rise again of a selfish element.

Science.gov (United States)

Burt, Austin; Koufopanou, Vassiliki

2004-12-01

Homing endonuclease genes (HEGs) are selfish genetic elements that spread by first cleaving chromosomes that do not contain them and then getting copied across to the broken chromosome as a byproduct of the repair process. The success of this strategy will depend on the opportunities for homing--in other words, the frequency with which HEG(+) and HEG(-) chromosomes come into contact--which varies widely among host taxa. HEGs are also unusual in that the selection pressure for endonuclease function disappears if they become fixed in a population, which makes them susceptible to degeneration and imposes a need for regular horizontal transmission between species. HEGs will be selected to reduce the harm done to the host organism, and this is expected to influence the evolution of their sequence specificity and maturase functions. HEGs may also be domesticated by their hosts, and are currently being put to human uses.

Dissipation induced asymmetric steering of distant atomic ensembles

Science.gov (United States)

Cheng, Guangling; Tan, Huatang; Chen, Aixi

2018-04-01

The asymmetric steering effects of separated atomic ensembles denoted by the effective bosonic modes have been explored by the means of quantum reservoir engineering in the setting of the cascaded cavities, in each of which an atomic ensemble is involved. It is shown that the steady-state asymmetric steering of the mesoscopic objects is unconditionally achieved via the dissipation of the cavities, by which the nonlocal interaction occurs between two atomic ensembles, and the direction of steering could be easily controlled through variation of certain tunable system parameters. One advantage of the present scheme is that it could be rather robust against parameter fluctuations, and does not require the accurate control of evolution time and the original state of the system. Furthermore, the double-channel Raman transitions between the long-lived atomic ground states are used and the atomic ensembles act as the quantum network nodes, which makes our scheme insensitive to the collective spontaneous emission of atoms.

A mean-field theory on the differential capacitance of asymmetric ionic liquid electrolytes

International Nuclear Information System (INIS)

Han, Yining; Huang, Shanghui; Yan, Tianying

2014-01-01

The size of ions significantly influences the electric double layer structure of room temperature ionic liquid (IL) electrolytes and their differential capacitance (C d ). In this study, we extended the mean-field theory (MFT) developed independently by Kornyshev (2007J. Phys. Chem. B 111 5545–57) and Kilic, Bazant, and Ajdari (2007 Phys. Rev. E 75 021502) (the KKBA MFT) to take into account the asymmetric 1:1 IL electrolytes by introducing an additional parameter ξ for the anion/cation volume ratio, besides the ionic compressibility γ in the KKBA MFT. The MFT of asymmetric ions becomes KKBA MFT upon ξ = 1, and further reduces to Gouy–Chapman theory in the γ → 0 limit. The result of the extended MFT demonstrates that the asymmetric ILs give rise to an asymmetric C d , with the higher peak in C d occurring at positive polarization for the smaller anionic size. At high potential, C d decays asymptotically toward KKBA MFT characterized by γ for the negative polarization, and characterized by ξγ for the positive polarization, with inverse-square-root behavior. At low potential, around the potential of zero charge, the asymmetric ions cause a higher C d , which exceeds that of Gouy–Chapman theory. (paper)

Nonlinear optical rectification and optical absorption in GaAs-Ga1-xAlxAs asymmetric double quantum wells: Combined effects of applied electric and magnetic fields and hydrostatic pressure

International Nuclear Information System (INIS)

Karabulut, I.; Mora-Ramos, M.E.; Duque, C.A.

2011-01-01

The intersubband electron-related nonlinear optical absorption and nonlinear optical rectification in GaAs-Ga 1-x Al x As asymmetric double quantum wells are studied, under the influence of combined or independent applied electric and magnetic fields as well as hydrostatic pressure. The outcome of the density matrix formalism and the effective mass, and parabolic-band approximations have been considered as main theoretical tools for the description. It is obtained that under particular geometrical conditions, with or without electric and/or magnetic field strength, the optical rectification is null and, simultaneously, in such circumstances the optical absorption has a relative maximum. It is also detected that the influence of the hydrostatic pressure leads to increasing or decreasing behaviors of the nonlinear optical absorption in dependence of the particular regime of pressure values considered, with significant distinction of the cases of opposite electric field orientations. - Highlights: → Maxima of the NOA correspond to zero in the NOR. → Electric fields can couple the double quantum wells. → Hydrostatic pressure can couple the double quantum wells. → NOA can increase/decrease with hydrostatic pressure. → Overlap between wave functions depends on the magnetic field.

Asymmetric Membranes Containing Micron-Size Silicon for High Performance Lithium Ion Battery Anode

International Nuclear Information System (INIS)

Byrd, Ian; Wu, Ji

2016-01-01

Micron-size Si anode is notorious for having extremely poor cycle life. It is mainly caused by the large volume change (∼300%) and poor mechanical strength of the Si electrode. Satisfying methods to address this issue are seriously lacking in literature. In this study, novel single-layer, double-layer and triple-layer asymmetric membranes containing micron-size silicon have been fabricated using a simple phase inversion method to dramatically improve its cyclability. The electrochemical performance of these asymmetric membranes as lithium ion battery anodes are evaluated and compared to pure micron-size Si powders and carbonaceous asymmetric membranes. All three types of asymmetric membrane electrodes demonstrate significantly enhanced stability as compared to pure Si powders. The single-layer asymmetric membrane has the largest capacity degradation due to the loss of pulverized Si powders from the membrane surface, only 40% of whose capacity can be retained in 100 cycles. But this performance is still much better than pure micron-size silicon electrode. After being coated with nanoporous carbonaceous layers on both sides of a single-layer asymmetric membrane to make a triple-layer asymmetric membrane (sandwich structure), the capacity retention is notably increased to 88% in 100 cycles at 610 mAh g"−"1 and 0.5C. The enhanced stability is attributed to the extra nanoporous coatings that can prevent the fractured Si powders from being leached out and allow facile lithium ion diffusions. Such a novel, efficient and scalable method may provide beneficiary guidance for designing high capacity lithium ion battery anodes with large volume change issues.

Restriction endonuclease analysis of chloroplast DNA in interspecies somatic Hybrids of Petunia.

Science.gov (United States)

Kumar, A; Cocking, E C; Bovenberg, W A; Kool, A J

1982-12-01

Restriction endonuclease cleavage pattern analysis of chloroplast DNA (cpDNA) of three different interspecific somatic hybrid plants revealed that the cytoplasms of the hybrids contained only cpDNA of P. parodii. The somatic hybrid plants analysed were those between P. parodii (wild type) + P. hybrida (wild type); P. parodii (wild type)+P. inflata (cytoplasmic albino mutant); P. parodii (wild type) + P. parviflora (nuclear albino mutant). The presence of only P. parodii chloroplasts in the somatic hybrid of P. parodii + P. inflata is possibly due to the stringent selection used for somatic hybrid production. However, in the case of the two other somatic hybrids P. parodii + P. hybrida and P. parodii + P. parviflora it was not possible to determine whether the presence of only P. parodii chloroplasts in these somatic hybrid plants was due to the nature of the selection schemes used or simply occurred by chance. The relevance of such somatic hybrid material for the study of genomic-cytoplasmic interaction is discussed, as well as the use of restriction endonuclease fragment patterns for the analysis of taxonomic and evolutionary inter-relationships in the genus Petunia.

Cleavage of DNA containing 5-fluorocytosine or 5-fluorouracil by type II restriction endonucleases

Czech Academy of Sciences Publication Activity Database

Olszewska, Agata; Daďová, Jitka; Mačková, Michaela; Hocek, Michal

2015-01-01

Roč. 23, č. 21 (2015), s. 6885-6890 ISSN 0968-0896 R&D Projects: GA ČR GA14-04289S Institutional support: RVO:61388963 Keywords : modified nucleotides * DNA * restriction endonucleases * DNA polymerase * pyrimidine nucleosides Subject RIV: CC - Organic Chemistry Impact factor: 2.923, year: 2015

Molecular dynamics simulations of deoxyribonucleic acids and repair enzyme T4 endonuclease V

International Nuclear Information System (INIS)

Pinak, Miroslav

1999-01-01

This report describes the results of molecular dynamics (MD) simulation of deoxyribonucleic acids (DNA) and specific repair enzyme T4 endonuclease V. Namely research described here is focused on the examination of specific recognition process, in which this repair enzyme recognizes the damaged site on the DNA molecule-thymine dimer (TD). TD is frequent DNA damage induced by UV radiation in sun light and unless properly repaired it may be mutagenic or lethal for cell, and is also considered among the major causes of skin cancer. T4 endonuclease V is a DNA specific repair enzyme from bacteriophage T4 that catalyzes the first reaction step of TD repair pathway. MD simulations of three molecules - native DNA dodecamer (12 base pairs), DNA of the same sequence of nucleotides as native one but with TD, and repair enzyme T4 endonuclease V - were performed for 1 ns individually for each molecule. Simulations were analyzed to determine the role of electrostatic interaction in the recognition process. It is found that electrostatic energies calculated for amino acids of the enzyme have positive values of around +15 kcal/mol. The electrostatic energy of TD site has negative value of approximately -9 kcal/mol, different from the nearly neutral value of the respective thymines site of the native DNA. The electrostatic interaction of TD site with surrounding water environment differs from the electrostatic interaction of other nucleotides. Differences found between TD site and respective thymines site of native DNA indicate that the electrostatic energy is an important factor contributing to proper recognition of TD site during scanning process in which enzyme scans the DNA. In addition to the electrostatic energy, the important factor in recognition process might be structural complementarity of enzyme and bent DNA with TD. There is significant kink formed around TD site, that is not observed in native DNA. (author)

RPA activates the XPF‐ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks

KAUST Repository

Abdullah, Ummi B

2017-06-13

During replication‐coupled DNA interstrand crosslink (ICL) repair, the XPF‐ERCC1 endonuclease is required for the incisions that release, or “unhook”, ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL. Here, we report that while purified XPF‐ERCC1 incises simple ICL‐containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single‐stranded DNA (ssDNA)‐binding replication protein A (RPA) selectively restores XPF‐ERCC1 endonuclease activity on this structure. The 5′–3′ exonuclease SNM1A can load from the XPF‐ERCC1‐RPA‐induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF‐ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo.

RPA activates the XPF‐ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks

KAUST Repository

Abdullah, Ummi B; McGouran, Joanna F; Brolih, Sanja; Ptchelkine, Denis; El‐Sagheer, Afaf H; Brown, Tom; McHugh, Peter J

2017-01-01

During replication‐coupled DNA interstrand crosslink (ICL) repair, the XPF‐ERCC1 endonuclease is required for the incisions that release, or “unhook”, ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL. Here, we report that while purified XPF‐ERCC1 incises simple ICL‐containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single‐stranded DNA (ssDNA)‐binding replication protein A (RPA) selectively restores XPF‐ERCC1 endonuclease activity on this structure. The 5′–3′ exonuclease SNM1A can load from the XPF‐ERCC1‐RPA‐induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF‐ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo.

Permeabilization of ultraviolet-irradiated chinese hamster cells with polyethylene glycol and introduction of ultraviolet endonuclease from Micrococcus luteus

International Nuclear Information System (INIS)

Yarosh, D.B.; Setlow, R.B.

1981-01-01

Chinese hamster V-79 cells were made permeable by treatment with polyethylene glycol and then incubated with a Micrococcus luteus extract containing ultraviolet-specific endonuclease activity. This treatment introduced nicks in irradiated, but not in unirradiated, deoxyribonucleic acid. The nicks remained open for at least 3 h; there was no loss of endonuclease-sensitive sites, and no excision of dimers as measured by chromatography was detected. In addition, there was no increase in ultraviolet resistance in treated cells. This suggests that the absence of a significant amount of excision repair in rodent cells is due to the lack of both incision and excision capacity

Improvement of the beam quality of a broad-area diode laser using double feedback from two external mirrors

DEFF Research Database (Denmark)

Chi, M.; Bøgh, A.-S.; Thestrup, B.

2004-01-01

In this letter, a symmetric double-feedback configuration, to improve the beam quality of broad-area diode lasers is demonstrated. With this configuration, a symmetric double-lobed far field can be obtained, and this configuration leads to good beam quality. The beam quality factor M-2 of a diode...... laser with the emitting area 1 mumx200 mum is improved by using both the asymmetric single feedback and the symmetric double feedback. M-2 values of 4.3 for the asymmetric single-feedback laser system and 3.3 for the symmetric double-feedback laser system are obtained, whereas the M-2 value...... of the freely running laser is 42. The far and the near fields are also measured and compared for the three conditions. (C) 2004 American Institute of Physics....

X-ray induced DNA double strand break production and repair in mammalian cells as measured by neutral filter elution

Energy Technology Data Exchange (ETDEWEB)

Bradley, M O; Kohn, K W [National Institutes of Health, Bethesda, MD (USA)

1979-10-01

A neutral filter elution method was used for detecting DNA double strand breaks in mouse L1210 cells after X-ray. The assay detected the number of double strand breaks induced by as little as 1000 rad of X-ray. The rate of DNA elution through the filters under neutral conditions increased with X-ray dose. Certain conditions for deproteinization, pH, and filter type were shown to increase the assay's sensitivity. Hydrogen peroxide and Bleomycin also induced apparent DNA double strand breaks, although the ratios of double to single strand breaks varied from those produced by X-ray. The introduction of double strand cuts by HpA I restriction endonuclease in DNA lysed on filters resulted in a rapid rate of elution under neutral conditions, implying that the method can detect double strand breaks if they exist in the DNA. The eluted DNA banded with a double stranded DNA marker in cesium chloride. This evidence suggested that the assay detected DNA double strand breaks. L1210 cells were shown to rejoin most of the DNA double strand breaks induced by 5-10 krad of X-ray with a half-time of about 40 minutes. (author).

Structural studies on metal-containing enzymes: T4 endonuclease VII and D. gigas formate dehydrogenase

NARCIS (Netherlands)

Raaijmakers, H.C.A.

2001-01-01

Many biological processes require metal ions, and many of these metal-ion functions involve metalloproteins. The metal ions in metalloproteins are often critical to the protein's function, structure, or stability. This thesis focuses on two of these proteins, bacteriophage T4 endonuclease

Asymmetric flows over symmetric surfaces: capacitive coupling in induced-charge electro-osmosis

Energy Technology Data Exchange (ETDEWEB)

Mansuripur, T S [Department of Physics, University of California, Santa Barbara, CA 93106 (United States); Pascall, A J; Squires, T M [Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 (United States)], E-mail: squires@engineering.ucsb.edu

2009-07-15

We report curious asymmetric induced-charge electro-osmotic (ICEO) flows over a symmetric, planar gate electrode under applied ac electric fields, whereas symmetric, counter-rotating rolls are expected. Furthermore, the asymmetric component of the flow is consistently directed towards the grounded electrode. We propose that capacitive coupling of the gate electrode to the microscope stage-a comparatively large equipotential surface that acts effectively as a ground-is responsible for this symmetry breaking. This stray capacitance drives the formation of a double layer whose zeta potential is proportional to the potential drop from the electrolyte directly above the gate electrode to the external stage. Therefore, the charge in this 'stray' double layer varies in phase with the driving field, resulting in a rectified, steady flow as with standard ICEO. We experimentally vary the stray capacitance, the electric potential of the stage and the location of the gate electrode, and find that the effect on the stray flow is qualitatively consistent with the predictions of the proposed mechanism. In the process, we demonstrate that capacitive coupling offers an additional means of manipulating fluid flow over a polarizable surface.

Asymmetric flows over symmetric surfaces: capacitive coupling in induced-charge electro-osmosis

International Nuclear Information System (INIS)

Mansuripur, T S; Pascall, A J; Squires, T M

2009-01-01

We report curious asymmetric induced-charge electro-osmotic (ICEO) flows over a symmetric, planar gate electrode under applied ac electric fields, whereas symmetric, counter-rotating rolls are expected. Furthermore, the asymmetric component of the flow is consistently directed towards the grounded electrode. We propose that capacitive coupling of the gate electrode to the microscope stage-a comparatively large equipotential surface that acts effectively as a ground-is responsible for this symmetry breaking. This stray capacitance drives the formation of a double layer whose zeta potential is proportional to the potential drop from the electrolyte directly above the gate electrode to the external stage. Therefore, the charge in this 'stray' double layer varies in phase with the driving field, resulting in a rectified, steady flow as with standard ICEO. We experimentally vary the stray capacitance, the electric potential of the stage and the location of the gate electrode, and find that the effect on the stray flow is qualitatively consistent with the predictions of the proposed mechanism. In the process, we demonstrate that capacitive coupling offers an additional means of manipulating fluid flow over a polarizable surface.

Lamb wave band gaps in a double-sided phononic plate

Science.gov (United States)

Wang, Peng; Chen, Tian-Ning; Yu, Kun-Peng; Wang, Xiao-Peng

2013-02-01

In this paper, we report on the theoretical investigation of the propagation characteristics of Lamb wave in a phononic crystal structure constituted by a square array of cylindrical stubs deposited on both sides of a thin homogeneous plate. The dispersion relations, the power transmission spectra, and the displacement fields of the eigenmodes are studied by using the finite-element method. We investigate the evolution of band gaps in the double-sided phononic plate with stub height on both sides arranged from an asymmetrical distribution to a symmetrical distribution gradually. Numerical results show that as the double stubs in a unit cell arranged more symmetrically on both sides, band width shifts, new band gaps appear, and the bands become flat due to localized resonant modes which couple with plate modes. Specially, more band gaps and flat bands can be found in the symmetrical system as a result of local resonances of the stubs which interact in a stronger way with the plate modes. Moreover, the symmetrical double-sided plate exhibits lower and smaller band gap than that of the asymmetrical plate. These propagation properties of elastic or acoustic waves in the double-sided plate can potentially be utilized to generate filters, slow the group velocity, low-frequency sound insulation, and design acoustic sensors.

Ultrasensitive electrochemical biosensor for detection of DNA from Bacillus subtilis by coupling target-induced strand displacement and nicking endonuclease signal amplification.

Science.gov (United States)

Hu, Yuhua; Xu, Xueqin; Liu, Qionghua; Wang, Ling; Lin, Zhenyu; Chen, Guonan

2014-09-02

A simple, ultrasensitive, and specific electrochemical biosensor was designed to determine the given DNA sequence of Bacillus subtilis by coupling target-induced strand displacement and nicking endonuclease signal amplification. The target DNA (TD, the DNA sequence from the hypervarient region of 16S rDNA of Bacillus subtilis) could be detected by the differential pulse voltammetry (DPV) in a range from 0.1 fM to 20 fM with the detection limit down to 0.08 fM at the 3s(blank) level. This electrochemical biosensor exhibits high distinction ability to single-base mismatch, double-bases mismatch, and noncomplementary DNA sequence, which may be expected to detect single-base mismatch and single nucleotide polymorphisms (SNPs). Moreover, the applicability of the designed biosensor for detecting the given DNA sequence from Bacillus subtilis was investigated. The result obtained by electrochemical method is approximately consistent with that by a real-time quantitative polymerase chain reaction detecting system (QPCR) with SYBR Green.

Scaling of cross-sections for asymmetric (e, 3e) process on helium ...

Indian Academy of Sciences (India)

An approximate simple scaling law is obtained for asymmetric (, 3) process on helium-like ions for double ionization by fast electrons. It is based on the equation ( Z ′ 3 / ) exp [ − Z ′ ( r 1 + r 2 ) ] , Z ′ = Z − ( 5 / 16 ) for ground state wave function of helium- like ions and Z ′ 2 scaling of energies. The scaling law is ...

Asymmetric dark matter, baryon asymmetry and lepton number violation

OpenAIRE

Frandsen, Mads T.; Hagedorn, Claudia; Huang, Wei-Chih; Molinaro, Emiliano; Päs, Heinrich

2018-01-01

We study the effect of lepton number violation (LNV) on baryon asymmetry, generated in the early Universe, in the presence of a dark sector with a global symmetry U(1)X , featuring asymmetric dark matter (ADM). We show that in general LNV, observable at the LHC or in neutrinoless double beta decay experiments, cannot wash out a baryon asymmetry generated at higher scales, unlike in scenarios without such dark sector. An observation of LNV at the TeV scale may thus support ADM scenarios. Consi...

Interaction of the E. coli DNA G:T-mismatch endonuclease (vsr protein) with oligonucleotides containing its target sequence.

Science.gov (United States)

Turner, D P; Connolly, B A

2000-12-15

The Escherichia coli vsr endonuclease recognises G:T base-pair mismatches in double-stranded DNA and initiates a repair pathway by hydrolysing the phosphate group 5' to the incorrectly paired T. The enzyme shows a preference for G:T mismatches within a particular sequence context, derived from the recognition site of the E. coli dcm DNA-methyltransferase (CC[A/T]GG). Thus, the preferred substrate for the vsr protein is (CT[A/T]GG), where the underlined T is opposed by a dG base. This paper provides quantitative data for the interaction of the vsr protein with a number of oligonucleotides containing G:T mismatches. Evaluation of specificity constant (k(st)/K(D); k(st)=rate constant for single turnover, K(D)=equilibrium dissociation constant) confirms vsr's preference for a G:T mismatch within a hemi-methylated dcm sequence, i.e. the best substrate is a duplex (both strands written in the 5'-3' orientation) composed of CT[A/T]GG and C(5Me)C[T/A]GG. Conversion of the mispaired T (underlined) to dU or the d(5Me)C to dC gave poorer substrates. No interaction was observed with oligonucleotides that lacked a G:T mismatch or did not possess a dcm sequence. An analysis of the fraction of active protein, by "reverse-titration" (i.e. adding increasing amounts of DNA to a fixed amount of protein followed by gel-mobility shift analysis) showed that less than 1% of the vsr endonuclease was able to bind to the substrate. This was confirmed using "competitive titrations" (where competitor oligonucleotides are used to displace a (32)P-labelled nucleic acid from the vsr protein) and burst kinetic analysis. This result is discussed in the light of previous in vitro and in vivo data which indicate that the MutL protein may be needed for full vsr activity. Copyright 2000 Academic Press.

Selective inhibition by methoxyamine of the apurinic/apyrimidinic endonuclease activity associated with pyrimidine dimer-DNA glycosylases from Micrococcus luteus and bacteriophage T4

International Nuclear Information System (INIS)

Liuzzi, M.; Weinfeld, M.; Paterson, M.C.

1987-01-01

The UV endonucleases from Micrococcus luteus and bacteriophage T4 possess two catalytic activities specific for the site of cyclobutane pyrimidine dimers in UV-irradiated DNA: a DNA glycosylase that cleaves the 5'-glycosyl bond of the dimerized pyrimidines and an apurinic/apyrimidinic (AP) endonuclease that thereupon incises the phosphodiester bond 3' to the resulting apyrimidinic site. The authors have explored the potential use of methoxyamine, a chemical that reacts at neutral pH with AP sites in DNA, as a selective inhibitor of the AP endonuclease activities residing in the M. luteus and T4 enzymes. The presence of 50 mM methoxyamine during incubation of UV-treated, [ 3 H]thymine-labeled poly(dA) x poly(dT) with either enzyme preparation was found to protect completely the irradiated copolymer from endonucleolytic attack at dimer sites, as assayed by yield of acid-soluble radioactivity. In contrast, the dimer-DNA glycosylase activity of each enzyme remained fully functional, as monitored retrospectively by release of free thymine after either photochemical-(5 kJ/m 2 , 254 nm) or photoenzymic- (Escherichia coli photolyase plus visible light) induced reversal of pyrimidine dimers in the UV-damaged substrate. The data demonstrate that the inhibition of the strand-incision reaction arises because of chemical modification of the AP sites and is not due to inactivation of the enzyme by methoxyamine. The results, combined with earlier findings for 5'-acting AP endonucleases, strongly suggest that methoxyamine is a highly specific inhibitor of virtually all AP endonucleases, irrespective of their modes of action, and may therefore prove useful in a wide variety of DNA repair studies

Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway.

Science.gov (United States)

Smith, Catherine E; Mendillo, Marc L; Bowen, Nikki; Hombauer, Hans; Campbell, Christopher S; Desai, Arshad; Putnam, Christopher D; Kolodner, Richard D

2013-10-01

Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.

Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway.

Directory of Open Access Journals (Sweden)

Catherine E Smith

2013-10-01

Full Text Available Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.

Experiments on ion acoustic typed double layers

International Nuclear Information System (INIS)

Chan, C.; Cho, M.H.; Intrator, T.; Hershkowitz, N.

1984-01-01

The formation of small amplitude double layers with potential drops the order of the electron temperature, was examined experimentally by pulsing a grid and thereby changing the electron drift across the target chamber of a triple plasma device. The rarefactive part of a long wavelength, low frequency ion wave grew in amplitude due to the presence of slowly drifting electrons. The corresponding current limitation led to the formation of the double layers. Depending on the plasma conditions, the asymmetric double layers either transform into a weak monotonic layer, a propagating shock, or a series of rarefactive solitary pulses. The rarefactive pulses propagate with Mach number less than one and resemble solitary plasma holes with density cavities in both the electron and the ion density profiles

Polymerase-endonuclease amplification reaction (PEAR for large-scale enzymatic production of antisense oligonucleotides.

Directory of Open Access Journals (Sweden)

Xiaolong Wang

Full Text Available Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain oligonucleotide is difficult to scale up because it requires expensive equipment, hazardous chemicals and a tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR, for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves over 100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation. PEAR has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs.

RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks.

Science.gov (United States)

Abdullah, Ummi B; McGouran, Joanna F; Brolih, Sanja; Ptchelkine, Denis; El-Sagheer, Afaf H; Brown, Tom; McHugh, Peter J

2017-07-14

During replication-coupled DNA interstrand crosslink (ICL) repair, the XPF-ERCC1 endonuclease is required for the incisions that release, or "unhook", ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL Here, we report that while purified XPF-ERCC1 incises simple ICL-containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single-stranded DNA (ssDNA)-binding replication protein A (RPA) selectively restores XPF-ERCC1 endonuclease activity on this structure. The 5'-3' exonuclease SNM1A can load from the XPF-ERCC1-RPA-induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF-ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo . © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Restriction endonuclease analysis of Pasteurella multocida isolates from three California turkey premises.

Science.gov (United States)

Christiansen, K H; Carpenter, T E; Snipes, K P; Hird, D W; Ghazikhanian, G Y

1992-01-01

Three California turkey premises that had repeated outbreaks of fowl cholera were studied for periods of 2 to 4 years. Using biochemical, serologic, plasmid DNA, and restriction endonuclease analyses of isolates of Pasteurella multocida from turkeys and wildlife on the premises, strains of the organism were found to be enzootic on two of the premises. On the third, a variety of strains of P. multocida were isolated from fowl cholera outbreak flocks.

Double layer for hard spheres with an off-center charge

Directory of Open Access Journals (Sweden)

W. Silvestre-Alcantara

2016-02-01

Full Text Available Simulations for the density and potential profiles of the ions in the planar electrical double layer of a model electrolyte or an ionic liquid are reported. The ions of a real electrolyte or an ionic liquid are usually not spheres; in ionic liquids, the cations are molecular ions. In the past, this asymmetry has been modelled by considering spheres that are asymmetric in size and/or valence (viz., the primitive model or by dimer cations that are formed by tangentially touching spheres. In this paper we consider spherical ions that are asymmetric in size and mimic the asymmetrical shape through an off-center charge that is located away from the center of the cation spheres, while the anion charge is at the center of anion spheres. The various singlet density and potential profiles are compared to (i the dimer situation, that is, the constituent spheres of the dimer cation are tangentially tethered, and (ii the standard primitive model. The results reveal the double layer structure to be substantially impacted especially when the cation is the counterion. As well as being of intrinsic interest, this off-center charge model may be useful for theories that consider spherical models and introduce the off-center charge as a perturbation.

Hamiltonian bifurcation perspective on two interacting vortex pairs: From symmetric to asymmetric leapfrogging, period doubling, and chaos

Science.gov (United States)

Whitchurch, Brandon; Kevrekidis, Panayotis G.; Koukouloyannis, Vassilis

2018-01-01

In this work we study the dynamical behavior of two interacting vortex pairs, each one of them consisting of two point vortices with opposite circulation in the two-dimensional plane. The vortices are considered as effective particles and their interaction can be described in classical mechanics terms. We first construct a Poincaré section, for a typical value of the energy, in order to acquire a picture of the structure of the phase space of the system. We divide the phase space in different regions which correspond to qualitatively distinct motions and we demonstrate its different temporal evolution in the "real" vortex space. Our main emphasis is on the leapfrogging periodic orbit, around which we identify a region that we term the "leapfrogging envelope" which involves mostly regular motions, such as higher order periodic and quasiperiodic solutions. We also identify the chaotic region of the phase plane surrounding the leapfrogging envelope as well as the so-called walkabout and braiding motions. Varying the energy as our control parameter, we construct a bifurcation tree of the main leapfrogging solution and its instabilities, as well as the instabilities of its daughter branches. We identify the symmetry-breaking instability of the leapfrogging solution (in line with earlier works), and also obtain the corresponding asymmetric branches of periodic solutions. We then characterize their own instabilities (including period doubling ones) and bifurcations in an effort to provide a more systematic perspective towards the types of motions available to this dynamical system.

Spin-polarizated transmissivity in an asymmetrical double barrier

International Nuclear Information System (INIS)

Teixeira, J D S; Frota, H O; Bittencourt, A C R

2014-01-01

The spin-polarized electron resonant tunnelling at zero magnetic field through a double barrier heterostructure like InAs/GaSb/InAs/GaSb/InAs has been calculated as a function of the electron energy. A model is proposed to study the combined effects of Dresselhaus and in-plane Rashba spin-orbit interactions on the spin-dependent tunnelling, taking into account the k 3 dependence of the Dresselhaus Hamiltonian. For the directions ϕ=45 ∘ and 135 ∘ the spin mixing produces a 100% efficiency of polarization. Moreover, the effect of the Dresselhaus and Rashba spin-orbit interactions are shown to be quite favorable for the fabrication of spin filters and spintronic devices. (paper)

Joint molecule resolution requires the redundant activities of MUS-81 and XPF-1 during Caenorhabditis elegans meiosis.

Directory of Open Access Journals (Sweden)

Nigel J O'Neil

Full Text Available The generation and resolution of joint molecule recombination intermediates is required to ensure bipolar chromosome segregation during meiosis. During wild type meiosis in Caenorhabditis elegans, SPO-11-generated double stranded breaks are resolved to generate a single crossover per bivalent and the remaining recombination intermediates are resolved as noncrossovers. We discovered that early recombination intermediates are limited by the C. elegans BLM ortholog, HIM-6, and in the absence of HIM-6 by the structure specific endonuclease MUS-81. In the absence of both MUS-81 and HIM-6, recombination intermediates persist, leading to chromosome breakage at diakinesis and inviable embryos. MUS-81 has an additional role in resolving late recombination intermediates in C. elegans. mus-81 mutants exhibited reduced crossover recombination frequencies suggesting that MUS-81 is required to generate a subset of meiotic crossovers. Similarly, the Mus81-related endonuclease XPF-1 is also required for a subset of meiotic crossovers. Although C. elegans gen-1 mutants have no detectable meiotic defect either alone or in combination with him-6, mus-81 or xpf-1 mutations, mus-81;xpf-1 double mutants are synthetic lethal. While mus-81;xpf-1 double mutants are proficient for the processing of early recombination intermediates, they exhibit defects in the post-pachytene chromosome reorganization and the asymmetric disassembly of the synaptonemal complex, presumably triggered by crossovers or crossover precursors. Consistent with a defect in resolving late recombination intermediates, mus-81; xpf-1 diakinetic bivalents are aberrant with fine DNA bridges visible between two distinct DAPI staining bodies. We were able to suppress the aberrant bivalent phenotype by microinjection of activated human GEN1 protein, which can cleave Holliday junctions, suggesting that the DNA bridges in mus-81; xpf-1 diakinetic oocytes are unresolved Holliday junctions. We propose that the

Nonmonotonous electron mobility due to structurally induced resonant coupling of subband states in an asymmetric double quantum well

Directory of Open Access Journals (Sweden)

R. K. Nayak

2015-11-01

Full Text Available We show that sharp nonmonotic variation of low temperature electron mobility μ can be achieved in GaAs/AlxGa1-xAs barrier delta-doped double quantum well structure due to quantum mechanical transfer of subband electron wave functions within the wells. We vary the potential profile of the coupled structure as a function of the doping concentration in order to bring the subbands into resonance such that the subband energy levels anticross and the eigen states of the coupled structure equally share both the wells thereby giving rise to a dip in mobility. When the wells are of equal widths, the dip in mobility occurs under symmetric doping of the side barriers. In case of unequal well widths, the resonance can be obtained by suitable asymmetric variation of the doping concentrations. The dip in mobility becomes sharp and also the wavy nature of mobility takes a rectangular shape by increasing the barrier width. We show that the dip in mobility at resonance is governed by the interface roughness scattering through step like changes in the subband mobilities. It is also gratifying to show that the drop in mobility at the onset of occupation of second subband is substantially supressed through the quantum mechanical transfer of subband wave functions between the wells. Our results can be utilized for performance enhancement of coupled quantum well devices.

Ultraviolet-endonuclease activity in cell extracts of Saccharomyces cerevisiae mutants defective in excision of pyrimidine dimers

International Nuclear Information System (INIS)

Bekker, M.L.; Kaboev, O.K.; Akhmedov, A.T.; Luchkina, L.A.

1980-01-01

Cell-free extracts of ultraviolet-sensitive mutants of Saccharomyces cerevisiae defective in excision of pyrimidine dimers, rad1, rad2, rad3, rad4, rad10, and rad16, as well as the extracts of the wild-type strain RAD+, display ultraviolet-endonuclease activity

Extreme bendability of DNA double helix due to bending asymmetry

NARCIS (Netherlands)

Salari, H.; Eslami-Mossallam, B.; Nederi, S.; Ejtehadi, M.R.

2015-01-01

Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for

The structure-specific endonuclease Ercc1-Xpf is required for targeted gene replacement in embryonic stem cells

NARCIS (Netherlands)

L.J. Niedernhofer (Laura); J. Essers (Jeroen); G. Weeda (Geert); H.B. Beverloo (Berna); J. de Wit (Jan); M. Muijtjens (Manja); H. Odijk (Hanny); J.H.J. Hoeijmakers (Jan); R. Kanaar (Roland)

2001-01-01

textabstractThe Ercc1-Xpf heterodimer, a highly conserved structure-specific endonuclease, functions in multiple DNA repair pathways that are pivotal for maintaining genome stability, including nucleotide excision repair, interstrand crosslink repair and homologous recombination. Erccl-Xpf incises

Charge reversal and surface charge amplification in asymmetric valence restricted primitive model planar electric double layers in the modified Poisson-Boltzmann theory

Directory of Open Access Journals (Sweden)

L.B. Bhuiyan

2017-12-01

Full Text Available The modified Poisson-Boltzmann theory of the restricted primitive model double layer is revisited and recast in a fresh, slightly broader perspective. Derivation of relevant equations follow the techniques utilized in the earlier MPB4 and MPB5 formulations and clarifies the relationship between these. The MPB4, MPB5, and a new formulation of the theory are employed in an analysis of the structure and charge reversal phenomenon in asymmetric 2:1/1:2 valence electrolytes. Furthermore, polarization induced surface charge amplification is studied in 3:1/1:3 systems. The results are compared to the corresponding Monte Carlo simulations. The theories are seen to predict the "exact" simulation data to varying degrees of accuracy ranging from qualitative to almost quantitative. The results from a new version of the theory are found to be of comparable accuracy as the MPB5 results in many situations. However, in some cases involving low electrolyte concentrations, theoretical artifacts in the form of un-physical "shoulders" in the singlet ionic distribution functions are observed.

Genetic recombination induced by DNA double-strand break in bacteriophage T4: nature of the left/right bias.

Science.gov (United States)

Shcherbakov, Victor P; Shcherbakova, Tamara; Plugina, Lidiya; Sizova, Svetlana; Kudryashova, Elena; Granovsky, Igor

2008-06-01

The experimental system combining double-strand breaks (DSBs), produced site-specifically by SegC endonuclease, with the famous advantages of the bacteriophage T4 rII mutant recombination analysis was used here to elucidate the origin of the recombination bias on two sides of the DSB, especially pronounced in gene 39 (topoisomerase II) and gene 59 (41-helicase loader) mutants. Three sources were found to contribute to the bias: (1) the SegC endonuclease may remain bound to the end of the broken DNA and thus protect it from exonuclease degradation; (2) in heteroduplex heterozygotes (HHs), arising as the recombinant products in the left-hand crosses, the transcribed strands are of rII mutant phenotype, so they, in contrast to the right-hand HHs, do not produce plaques on the lawn of the lambda-lysogenic host; and (3) the intrinsic polarity of T4 chromosome, reflected in transcription, may be a cause for discrimination of promoter-proximal and promoter-distal DNA sequences. It is shown that the apparent recombination bias does not imply one-sidedness of the DSB repair but just reflects a different depth of the end processing. It is inferred that the cause, underlying the "intrinsic" bias, might be interference between strand exchange and transcription. Topoisomerase and helicase functions are necessary to turn the process in favor of strand exchange. The idea is substantiated that the double-stranded to single-stranded DNA transition edge (not ss-DNA tip) serves as an actual recombinogenic element.

The transition mechanism from a symmetric single period discharge to a period-doubling discharge in atmospheric helium dielectric-barrier discharge

International Nuclear Information System (INIS)

Zhang, Dingzong; Wang, Yanhui; Wang, Dezhen

2013-01-01

Period-doubling and chaos phenomenon have been frequently observed in atmospheric-pressure dielectric-barrier discharges. However, how a normal single period discharge bifurcates into period-doubling state is still unclear. In this paper, by changing the driving frequency, we study numerically the transition mechanisms from a normal single period discharge to a period-doubling state using a one-dimensional self-consistent fluid model. The results show that before a discharge bifurcates into a period-doubling state, it first deviates from its normal operation and transforms into an asymmetric single period discharge mode. Then the weaker discharge in this asymmetric discharge will be enhanced gradually with increasing of the frequency until it makes the subsequent discharge weaken and results in the discharge entering a period-doubling state. In the whole transition process, the spatial distribution of the charged particle density and the electric field plays a definitive role. The conclusions are further confirmed by changing the gap width and the amplitude of the applied voltage

The transition mechanism from a symmetric single period discharge to a period-doubling discharge in atmospheric helium dielectric-barrier discharge

Energy Technology Data Exchange (ETDEWEB)

Zhang, Dingzong; Wang, Yanhui; Wang, Dezhen [School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116024 (China)

2013-06-15

Period-doubling and chaos phenomenon have been frequently observed in atmospheric-pressure dielectric-barrier discharges. However, how a normal single period discharge bifurcates into period-doubling state is still unclear. In this paper, by changing the driving frequency, we study numerically the transition mechanisms from a normal single period discharge to a period-doubling state using a one-dimensional self-consistent fluid model. The results show that before a discharge bifurcates into a period-doubling state, it first deviates from its normal operation and transforms into an asymmetric single period discharge mode. Then the weaker discharge in this asymmetric discharge will be enhanced gradually with increasing of the frequency until it makes the subsequent discharge weaken and results in the discharge entering a period-doubling state. In the whole transition process, the spatial distribution of the charged particle density and the electric field plays a definitive role. The conclusions are further confirmed by changing the gap width and the amplitude of the applied voltage.

Geographically diverse Australian isolates of Melissococcus pluton exhibit minimal genotypic diversity by restriction endonuclease analysis.

Science.gov (United States)

Djordjevic, S P; Smith, L A; Forbes, W A; Hornitzky, M A

1999-04-15

Melissococcus pluton, the causative agent of European foulbrood is an economically significant disease of honey bees (Apis mellifera) across most regions of the world and is prevalent throughout most states of Australia. 49 Isolates of M. pluton recovered from diseased colonies or honey samples in New South Wales, Queensland, South Australia, Tasmania and Victoria were compared using SDS-PAGE, Western immunoblotting and restriction endonuclease analyses. DNA profiles of all 49 geographically diverse isolates showed remarkably similar AluI profiles although four isolates (one each from Queensland, South Australia, New South Wales and Victoria) displayed minor profile variations compared to AluI patterns of all other isolates. DNA from a subset of the 49 Australian and three isolates from the United Kingdom were digested separately with the restriction endonucleases CfoI, RsaI and DraI. Restriction endonuclease fragment patterns generated using these enzymes were also similar although minor variations were noted. SDS-PAGE of whole cell proteins from 13 of the 49 isolates from different states of Australia, including the four isolates which displayed minor profile variations (AluI) produced indistinguishable patterns. Major immunoreactive proteins of approximate molecular masses of 21, 24, 28, 30, 36, 40, 44, 56, 60, 71, 79 and 95 kDa were observed in immunoblots of whole cell lysates of 22 of the 49 isolates and reacted with rabbit hyperimmune antibodies raised against M. pluton whole cells. Neither SDS-PAGE or immunoblotting was capable of distinguishing differences between geographically diverse isolates of M. pluton. Collectively these data confirm that Australian isolates of M. pluton are genetically homogeneous and that this species may be clonal. Plasmid DNA was not detected in whole cell DNA profiles of any isolate resolved using agarose gel electrophoresis.

Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System*

Science.gov (United States)

Smith, Catherine E.; Bowen, Nikki; Graham, William J.; Goellner, Eva M.; Srivatsan, Anjana; Kolodner, Richard D.

2015-01-01

Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5′ nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3′ nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg2+ and Mn2+ for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR. PMID:26170454

Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System.

Science.gov (United States)

Smith, Catherine E; Bowen, Nikki; Graham, William J; Goellner, Eva M; Srivatsan, Anjana; Kolodner, Richard D

2015-08-28

Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5' nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3' nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg(2+) and Mn(2+) for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Purification and characterization of VDE, a site-specific endonuclease from the yeast Saccharomyces cerevisiae.

Science.gov (United States)

Gimble, F S; Thorner, J

1993-10-15

The 119-kDa primary translation product of the VMA1 gene of Saccharomyces cerevisiae undergoes a self-catalyzed rearrangement ("protein splicing") that excises an internal 50-kDa segment of the polypeptide and joins the amino-terminal and carboxyl-terminal segments to generate the 69-kDa subunit of the vacuolar membrane-associated H(+)-ATPase. We have shown previously that the internal segment is a site-specific endonuclease (Gimble, F. S., and Thorner, J. (1992) Nature 357, 301-306). Here we describe methods for the high level expression and purification to near homogeneity of both the authentic VMA1-derived endonuclease (or VDE) from yeast (yield 18%) and a recombinant form of VDE made in bacteria (yield 29%). Detailed characterization of these preparations demonstrated that the yeast-derived and bacterially produced enzymes were indistinguishable, as judged by: (a) behavior during purification; (b) apparent native molecular mass (50 kDa); (c) immunological reactivity; and (d) catalytic properties (specific activity; cleavage site recognition; and optima for pH, temperature, divalent cation and ionic strength). The minimal site required for VDE cleavage was delimited to a 30-base pair sequence within its specific substrate (the VMA1 delta vde allele).

Order, viscoelastic, and dielectric properties of symmetric and asymmetric alkyl[1]benzothieno[3,2-b][1]benzothiophenes.

Science.gov (United States)

Grigoriadis, Christos; Niebel, Claude; Ruzié, Christian; Geerts, Yves H; Floudas, George

2014-02-06

The morphology, the viscoelastic, the dielectric properties and the dynamics of phase transformation are studied in symmetrically and asymmetrically substituted alkyl[1]benzothieno[3,2-b][1]benzothiophenes (C8-BTBT) by X-ray scattering, rheology, and dielectric spectroscopy. The interlayer spacing reflects the molecular and supramolecular ordering, respectively, in the symmetrically and asymmetrically substituted BTBTs. In the asymmetric BTBT, the core layer is double in size with a broader network of intermolecular interactions though the increased S-S contacts that is prerequisite for the development of high performance OFET devices. Two crystal states with elastic and viscoelastic responses were identified in the symmetric compound. In contrast, the SmA phase in the asymmetric compound is a viscoelastic solid. A path-dependent dielectric environment with a switchable dielectric permittivity was found in both compounds by cooling below 0 °C with possible implications to charge transport. The kinetics of phase transformation to the crystalline and SmA phases revealed a nucleation and growth mechanism with rates dominated by the low activation barriers.

Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii.

Science.gov (United States)

Matsui, Eriko; Abe, Junko; Yokoyama, Hideshi; Matsui, Ikuo

2004-04-16

Flap endonuclease-1 (FEN-1) possessing 5'-flap endonuclease and 5'-->3' exonuclease activity plays important roles in DNA replication and repair. In this study, the kinetic parameters of mutants at highly conserved aromatic residues, Tyr33, Phe35, Phe79, and Phe278-Phe279, in the vicinity of the catalytic centers of FEN-1 were examined. The substitution of these aromatic residues with alanine led to a large reduction in kcat values, although these mutants retained Km values similar to that of the wild-type enzyme. Notably, the kcat of Y33A and F79A decreased 333-fold and 71-fold, respectively, compared with that of the wild-type enzyme. The aromatic residues Tyr33 and Phe79, and the aromatic cluster Phe278-Phe279 mainly contributed to the recognition of the substrates without the 3' projection of the upstream strand (the nick, 5'-recess-end, single-flap, and pseudo-Y substrates) for the both exo- and endo-activities, but played minor roles in recognizing the substrates with the 3' projection (the double flap substrate and the nick substrate with the 3' projection). The replacement of Tyr33, Phe79, and Phe278-Phe279, with non-charged aromatic residues, but not with aliphatic hydrophobic residues, recovered the kcat values almost fully for the substrates without the 3' projection of the upstream strand, suggesting that the aromatic groups of Tyr33, Phe79, and Phe278-Phe279 might be involved in the catalytic reaction, probably via multiple stacking interactions with nucleotide bases. The stacking interactions of Tyr33 and Phe79 might play important roles in fixing the template strand and the downstream strand, respectively, in close proximity to the active center to achieve the productive transient state leading to the hydrolysis.

Biochemical characterization of recombinant influenza A polymerase heterotrimer complex: Endonuclease activity and evaluation of inhibitors

Czech Academy of Sciences Publication Activity Database

Xing, W.; Barauskas, O.; Kirschberg, T.; Niedziela-Majka, A.; Clarke, M.; Birkuš, Gabriel; Weissburg, P.; Liu, X.; Schultz, B. E.; Sakowicz, R.; Kwon, H. J.; Feng, J. Y.

2017-01-01

Roč. 12, č. 8 (2017), č. článku e0181969. E-ISSN 1932-6203 Institutional support: RVO:61388963 Keywords : virus PA endonuclease * respiratory syncytial virus * RNA synthesis Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 2.806, year: 2016 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181969

An ultrasensitive colorimeter assay strategy for p53 mutation assisted by nicking endonuclease signal amplification.

Science.gov (United States)

Lin, Zhenyu; Yang, Weiqiang; Zhang, Guiyun; Liu, Qida; Qiu, Bin; Cai, Zongwei; Chen, Guonan

2011-08-28

A novel catalytic colorimetric assay assisted by nicking endonuclease signal amplification (NESA) was developed. With the signal amplification, the detection limit of the p53 target gene can be as low as 1 pM, which is nearly 5 orders of magnitude lower than that of other previously reported colorimetric DNA detection strategies based on catalytic DNAzyme.

Double Fano resonances in plasmon coupling nanorods

International Nuclear Information System (INIS)

Liu, Fei; Jin, Jie

2015-01-01

Fano resonances are investigated in nanorods with symmetric lengths and side-by-side assembly. Single Fano resonance can be obtained by a nanorod dimer, and double Fano resonances are shown in nanorod trimers with side-by-side assembly. With transverse plasmon excitation, Fano resonances are caused by the destructive interference between a bright superradiant mode and dark subradiant modes. The bright mode originates from the electric plasmon resonance, and the dark modes originate from the magnetic resonances induced by near-field inter-rod coupling. Double Fano resonances result from double dark modes at different wavelengths, which are induced and tuned by the asymmetric gaps between the adjacent nanorods. Fano resonances show a high figure of merit and large light extinction in the periodic array of assembled nanorods, which can potentially be used in multiwavelength sensing in the visible and near-infrared regions. (paper)

Asymmetric carbon nanotube-MnO2 two-ply yarn supercapacitors for wearable electronics

Science.gov (United States)

Su, Fenghua; Miao, Menghe

2014-04-01

Strong and flexible two-ply carbon nanotube yarn supercapacitors are electrical double layer capacitors that possess relatively low energy storage capacity. Pseudocapacitance metal oxides such as MnO2 are well known for their high electrochemical performance and can be coated on carbon nanotube yarns to significantly improve the performance of two-ply carbon nanotube yarn supercapacitors. We produced a high performance asymmetric two-ply yarn supercapacitor from as-spun CNT yarn and CNT@MnO2 composite yarn in aqueous electrolyte. The as-spun CNT yarn serves as negative electrode and the CNT@MnO2 composite yarn as positive electrode. This asymmetric architecture allows the operating potential window to be extended from 1.0 to 2.0 V and results in much higher energy and power densities than the reference symmetric two-ply yarn supercapacitors, reaching 42.0 Wh kg-1 at a lower power density of 483.7 W kg-1, and 28.02 Wh kg-1 at a higher power density of 19 250 W kg-1. The asymmetric supercapacitor can sustain cyclic charge-discharge and repeated folding/unfolding actions without suffering significant deterioration of specific capacitance. The combination of high strength, flexibility and electrochemical performance makes the asymmetric two-ply yarn supercapacitor a suitable power source for flexible electronic devices for applications that require high durability and wearer comfort.

Asymmetric epigenetic modification and elimination of rDNA sequences by polyploidization in wheat.

Science.gov (United States)

Guo, Xiang; Han, Fangpu

2014-11-01

rRNA genes consist of long tandem repeats clustered on chromosomes, and their products are important functional components of the ribosome. In common wheat (Triticum aestivum), rDNA loci from the A and D genomes were largely lost during the evolutionary process. This biased DNA elimination may be related to asymmetric transcription and epigenetic modifications caused by the polyploid formation. Here, we observed both sets of parental nucleolus organizing regions (NORs) were expressed after hybridization, but asymmetric silencing of one parental NOR was immediately induced by chromosome doubling, and reversing the ploidy status could not reactivate silenced NORs. Furthermore, increased CHG and CHH DNA methylation on promoters was accompanied by asymmetric silencing of NORs. Enrichment of H3K27me3 and H3K9me2 modifications was also observed to be a direct response to increased DNA methylation and transcriptional inactivation of NOR loci. Both A and D genome NOR loci with these modifications started to disappear in the S4 generation and were completely eliminated by the S7 generation in synthetic tetraploid wheat. Our results indicated that asymmetric epigenetic modification and elimination of rDNA sequences between different donor genomes may lead to stable allopolyploid wheat with increased differentiation and diversity. © 2014 American Society of Plant Biologists. All rights reserved.

Identification and characterization of inhibitors of human apurinic/apyrimidinic endonuclease APE1.

Directory of Open Access Journals (Sweden)

Anton Simeonov

2009-06-01

Full Text Available APE1 is the major nuclease for excising abasic (AP sites and particular 3'-obstructive termini from DNA, and is an integral participant in the base excision repair (BER pathway. BER capacity plays a prominent role in dictating responsiveness to agents that generate oxidative or alkylation DNA damage, as well as certain chain-terminating nucleoside analogs and 5-fluorouracil. We describe within the development of a robust, 1536-well automated screening assay that employs a deoxyoligonucleotide substrate operating in the red-shifted fluorescence spectral region to identify APE1 endonuclease inhibitors. This AP site incision assay was used in a titration-based high-throughput screen of the Library of Pharmacologically Active Compounds (LOPAC(1280, a collection of well-characterized, drug-like molecules representing all major target classes. Prioritized hits were authenticated and characterized via two high-throughput screening assays -- a Thiazole Orange fluorophore-DNA displacement test and an E. coli endonuclease IV counterscreen -- and a conventional, gel-based radiotracer incision assay. The top, validated compounds, i.e. 6-hydroxy-DL-DOPA, Reactive Blue 2 and myricetin, were shown to inhibit AP site cleavage activity of whole cell protein extracts from HEK 293T and HeLa cell lines, and to enhance the cytotoxic and genotoxic potency of the alkylating agent methylmethane sulfonate. The studies herein report on the identification of novel, small molecule APE1-targeted bioactive inhibitor probes, which represent initial chemotypes towards the development of potential pharmaceuticals.

Cell division genes promote asymmetric interaction between Numb and Notch in the Drosophila CNS.

Science.gov (United States)

Wai, P; Truong, B; Bhat, K M

1999-06-01

Cell intrinsic and cell extrinsic factors mediate asymmetric cell divisions during neurogenesis in the Drosophila embryo. In the NB4-2->GMC-1->RP2/sib lineage, one of the well-studied neuronal lineages in the ventral nerve cord, the Notch (N) signaling interacts with the asymmetrically localized Numb (Nb) to specify sibling neuronal fates to daughter cells of GMC-1. In this current study, we have investigated asymmetric cell fate specifications by N and Nb in the context of cell cycle. We have used loss-of-function mutations in N and nb, cell division mutants cyclinA (cycA), regulator of cyclin A1 (rca1) and string/cdc25 phosphatase (stg), and the microtubule destabilizing agent, nocodazole, to investigate this issue. We report that the loss of cycA, rca1 or stg leads to a block in the division of GMC-1, however, this GMC-1 exclusively adopts an RP2 identity. While the loss of N leads to the specification of RP2 fates to both progeny of GMC-1 and loss of nb results in the specification of sib fates to these daughter cells, the GMC-1 in the double mutant between nb and cycA assumes a sib fate. These epistasis results indicate that both N and nb function downstream of cell division genes and that progression through cell cycle is required for the asymmetric localization of Nb. In the absence of entry to metaphase, the Nb protein prevents the N signaling from specifying sib fate to the RP2/sib precursor. These results are also consistent with our finding that the sib cell is specified as RP2 in N; nb double mutants. Finally, our results show that nocodazole-arrested GMC-1 in wild-type embryos randomly assumes either an RP2 fate or a sib fate. This suggests that microtubules are involved in mediating the antagonistic interaction between Nb and N during RP2 and sib fate specification.

Asymmetric Electrodes Constructed with PAN-Based Activated Carbon Fiber in Capacitive Deionization

Directory of Open Access Journals (Sweden)

Mingzhe Li

2014-01-01

Full Text Available Capacitive deionization (CDI method has drawn much attention for its low energy consumption, low pollution, and convenient manipulation. Activated carbon fibers (ACFs possess high adsorption ability and can be used as CDI electrode material. Herein, two kinds of PAN-based ACFs with different specific surface area (SSA were used for the CDI electrodes. The CDI performance was investigated; especially asymmetric electrodes’ effect was evaluated. The results demonstrated that PAN-based ACFs showed a high electrosorption rate (complete electrosorption in less than half an hour and moderate electrosorption capacity (up to 0.2 mmol/g. CDI experiments with asymmetric electrodes displayed a variation in electrosorption capacity between forward voltage and reverse voltage. It can be attributed to the electrical double layer (EDL overlap effect and inner pore potential; thus the ions with smaller hydrated ionic radius can be adsorbed more easily.

Does asymmetric correlation affect portfolio optimization?

Science.gov (United States)

Fryd, Lukas

2017-07-01

The classical portfolio optimization problem does not assume asymmetric behavior of relationship among asset returns. The existence of asymmetric response in correlation on the bad news could be important information in portfolio optimization. The paper applies Dynamic conditional correlation model (DCC) and his asymmetric version (ADCC) to propose asymmetric behavior of conditional correlation. We analyse asymmetric correlation among S&P index, bonds index and spot gold price before mortgage crisis in 2008. We evaluate forecast ability of the models during and after mortgage crisis and demonstrate the impact of asymmetric correlation on the reduction of portfolio variance.

Creation of targeted inversion mutations in plants using an RNA-guided endonuclease

Institute of Scientific and Technical Information of China (English)

Congsheng Zhang; Changlin Liu; Jianfeng Weng; Beijiu Cheng; Fang Liu; Xinhai Li; Chuanxiao Xie

2017-01-01

Inversions are DNA rearrangements that are essential for plant gene evolution and adaptation to environmental changes. We demonstrate the creation of targeted inversions and previously reported targeted deletion mutations via delivery of a pair of RNA-guided endonucleases (RGENs) of CRISPR/Cas9. The efficiencies of the targeted inversions were 2.6%and 2.2%in the Arabidopsis FLOWERING TIME (AtFT) and TERMINAL FLOWER 1 (AtTFL1) loci, respectively. Thus, we successfully established an approach that can potentially be used to introduce targeted DNA inversions of interest for functional studies and crop improvement.

Alteration of Sequence Specificity of the Type IIS Restriction Endonuclease BtsI

OpenAIRE

Guan, Shengxi; Blanchard, Aine; Zhang, Penghua; Zhu, Zhenyu

2010-01-01

The Type IIS restriction endonuclease BtsI recognizes and digests at GCAGTG(2/0). It comprises two subunits: BtsIA and BtsIB. The BtsIB subunit contains the recognition domain, one catalytic domain for bottom strand nicking and part of the catalytic domain for the top strand nicking. BtsIA has the rest of the catalytic domain that is responsible for the DNA top strand nicking. BtsIA alone has no activity unless it mixes with BtsIB to reconstitute the BtsI activity. During characterization of ...

A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I

Czech Academy of Sciences Publication Activity Database

Šišáková, Eva; Stanley, L. K.; Weiserová, Marie; Szczelkun, M. D.

2008-01-01

Roč. 36, č. 12 (2008), s. 1-11 ISSN 0305-1048 R&D Projects: GA ČR GA204/07/0325 Grant - others:XE(XE) BioNano-Switch 043288 Institutional research plan: CEZ:AV0Z50200510 Keywords : restriction endonuclease * mutagenesis * dsdna Subject RIV: EE - Microbiology, Virology Impact factor: 6.878, year: 2008

Atypical myxomatosis--virus isolation, experimental infection of rabbits and restriction endonuclease analysis of the isolate.

Science.gov (United States)

Psikal, I; Smíd, B; Rodák, L; Valícek, L; Bendová, J

2003-08-01

Atypical form of myxomatosis, which caused non-lethal and clinically mild disease in domestic rabbits 1 month after immunization with a commercially available vaccine MXT, is described. The isolated myxoma virus designated as Litovel 2 (Li-2) did not induce systemic disease following subcutaneous and intradermal applications in susceptible experimental rabbits but led to the immune response demonstrated by ELISA. No severe disease was induced in those Li-2 inoculated rabbits by challenge with the virulent strains Lausanne (Lu) or Sanar (SA), while the control animals showed nodular form of myxomatosis with lethal course of the illness. Restriction fragment length polymorphism (RFLP) of genomic DNA with KpnI and BamHI endonucleases was used for genetic characterization of the Li-2 isolate, the vaccine strain MXT and both virulent strains Lu and SA, respectively. In general, RFLP analysis has shown to be informative for inferring genetic relatedness between myxoma viruses. Based on restriction endonuclease DNA fragment size distribution, it was evident that the pathogenic strain SA is genetically related to the reference strain Lu and the isolate Li-2 is more related, but not identical, to the vaccination strain MXT.

Single substitution in bacteriophage T4 RNase H alters the ratio between its exo- and endonuclease activities.

Science.gov (United States)

Kholod, Natalia; Sivogrivov, Dmitry; Latypov, Oleg; Mayorov, Sergey; Kuznitsyn, Rafail; Kajava, Andrey V; Shlyapnikov, Mikhail; Granovsky, Igor

2015-11-01

The article describes substitutions in bacteriophage T4 RNase H which provide so called das-effect. Phage T4 DNA arrest suppression (das) mutations have been described to be capable of partially suppressing the phage DNA arrest phenotype caused by a dysfunction in genes 46 and/or 47 (also known as Mre11/Rad50 complex). Genetic mapping of das13 (one of the das mutations) has shown it to be in the region of the rnh gene encoding RNase H. Here we report that Das13 mutant of RNase H has substitutions of valine 43 and leucine 242 with isoleucines. To investigate the influence of these mutations on RNase H nuclease properties we have designed a novel in vitro assay that allows us to separate and quantify exo- or endonuclease activities of flap endonuclease. The nuclease assay in vitro showed that V43I substitution increased the ratio between exonuclease/endonuclease activities of RNase H whereas L242I substitution did not affect the nuclease activity of RNase H in vitro. However, both mutations were necessary for the full das effect in vivo. Molecular modelling of the nuclease structure suggests that V43I substitution may lead to disposition of H4 helix, responsible for the interaction with the first base pairs of 5'end of branched DNA. These structural changes may affect unwinding of the first base pairs of gapped or nicked DNA generating a short flap and therefore may stabilize the DNA-enzyme complex. L242I substitution did not affect the structure of RNase H and its role in providing das-effect remains unclear. Copyright © 2015 Elsevier B.V. All rights reserved.

Asymmetric cation-binding catalysis

DEFF Research Database (Denmark)

Oliveira, Maria Teresa; Lee, Jiwoong

2017-01-01

The employment of metal salts is quite limited in asymmetric catalysis, although it would provide an additional arsenal of safe and inexpensive reagents to create molecular functions with high optical purity. Cation chelation by polyethers increases the salts' solubility in conventional organic...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...... highly enantioselective silylation reactions in polyether-generated chiral environments, and leading to a record-high turnover in asymmetric organocatalysis. This can lead to further applications by the asymmetric use of other inorganic salts in various organic transformations....

PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus. II. Characterization Of the binding and cleavage abilities by site-directed mutagenesis.

OpenAIRE

Komori, K; Ichiyanagi, K; Morikawa, K; Ishino, Y

1999-01-01

PI- Pfu I and PI- Pfu II from Pyrococcus furiosus are homing endonucleases, as shown in the accompanying paper. These two endonucleases are produced by protein splicing from the precursor protein including ribonucleotide reductase (RNR). We show here that both enzymes specifically interact with their substrate DNA and distort the DNA strands by 73 degrees and 67 degrees, respectively. They have two copies of the amino acid sequence motif LAGLIDADG, which is present in the majority of homing e...

Role of asymmetries in the chaotic dynamics of the double-well ...

Indian Academy of Sciences (India)

Duffing oscillator driven by a periodic force with three different forms of asymmetrical double-well potentials is considered. Three forms of asymmetry are introduced by varying the depth of the left-well alone, location of the minimum of the left-well alone and above both the potentials. Applying the Melnikov method, the ...

Asymmetric carbon nanotube–MnO2 two-ply yarn supercapacitors for wearable electronics

International Nuclear Information System (INIS)

Su, Fenghua; Miao, Menghe

2014-01-01

Strong and flexible two-ply carbon nanotube yarn supercapacitors are electrical double layer capacitors that possess relatively low energy storage capacity. Pseudocapacitance metal oxides such as MnO 2 are well known for their high electrochemical performance and can be coated on carbon nanotube yarns to significantly improve the performance of two-ply carbon nanotube yarn supercapacitors. We produced a high performance asymmetric two-ply yarn supercapacitor from as-spun CNT yarn and CNT@MnO 2 composite yarn in aqueous electrolyte. The as-spun CNT yarn serves as negative electrode and the CNT@MnO 2 composite yarn as positive electrode. This asymmetric architecture allows the operating potential window to be extended from 1.0 to 2.0 V and results in much higher energy and power densities than the reference symmetric two-ply yarn supercapacitors, reaching 42.0 Wh kg −1 at a lower power density of 483.7 W kg −1 , and 28.02 Wh kg −1 at a higher power density of 19 250 W kg −1 . The asymmetric supercapacitor can sustain cyclic charge–discharge and repeated folding/unfolding actions without suffering significant deterioration of specific capacitance. The combination of high strength, flexibility and electrochemical performance makes the asymmetric two-ply yarn supercapacitor a suitable power source for flexible electronic devices for applications that require high durability and wearer comfort. (paper)

Observation of asymmetric transverse voltage in granular high-T c superconductors

International Nuclear Information System (INIS)

Luz, M.S. da; Carvalho, F.J.H. de; Santos, C.A.M. dos; Shigue, C.Y.; Machado, A.J.S.; Ricardo da Silva, R.

2005-01-01

This work reports the influence of the granularity on the transverse voltage as a function of the temperature, V XY (T), in polycrystalline samples of Bi 2 Sr 2 Ca 0.8 Pr 0.2 Cu 2 O 8+δ composition. It is observed nonzero transverse voltage at zero external magnetic field in the vicinity of the superconducting transition while far away from it, both above and below, no such voltage was detected. Measurements of V XY (T) in both directions of magnetic field allowed to calculate the symmetric and asymmetric transverse voltages in the full range of the applied magnetic field studied (zero up to 9 T). The symmetric transverse voltage as a function of the temperature presents sign reversal of the Hall resistance and positive Hall voltage at normal state such as expected for hole-doped high critical temperature superconductors. On the other hand, the asymmetric component of V XY (T) shows a peak near the superconducting transition which has been recently reported in literature. V XY (T) curves measured in a sample with double superconducting transition, which was confirmed by ac-susceptibility measurements and hysteresis loops of the magneto-resistance, present two peaks in the asymmetric component. These peaks are related to the intergranular and intragranular transitions and can be explained within the framework of Josephson and Abrikosov vortices and anti-vortices motion. By comparing the temperature dependence of the asymmetric transverse voltage and the derivative of longitudinal voltage is possible to observe a specific relation between both transport properties, which is noted to be valid not only at zero applied magnetic field but also under applied field

Selective metal binding to Cys-78 within endonuclease V causes an inhibition of catalytic activities without altering nontarget and target DNA binding

International Nuclear Information System (INIS)

Prince, M.A.; Friedman, B.; Gruskin, E.A.; Schrock, R.D. III; Lloyd, R.S.

1991-01-01

T4 endonuclease V is a pyrimidine dimer-specific DNA repair enzyme which has been previously shown not to require metal ions for either of its two catalytic activities or its DNA binding function. However, we have investigated whether the single cysteine within the enzyme was able to bind metal salts and influence the various activities of this repair enzyme. A series of metals (Hg2+, Ag+, Cu+) were shown to inactivate both endonuclease Vs pyrimidine dimer-specific DNA glycosylase activity and the subsequent apurinic nicking activity. The binding of metal to endonuclease V did not interfere with nontarget DNA scanning or pyrimidine dimer-specific binding. The Cys-78 codon within the endonuclease V gene was changed by oligonucleotide site-directed mutagenesis to Thr-78 and Ser-78 in order to determine whether the native cysteine was directly involved in the enzyme's DNA catalytic activities and whether the cysteine was primarily responsible for the metal binding. The mutant enzymes were able to confer enhanced ultraviolet light (UV) resistance to DNA repair-deficient Escherichia coli at levels equal to that conferred by the wild type enzyme. The C78T mutant enzyme was purified to homogeneity and shown to be catalytically active on pyrimidine dimer-containing DNA. The catalytic activities of the C78T mutant enzyme were demonstrated to be unaffected by the addition of Hg2+ or Ag+ at concentrations 1000-fold greater than that required to inhibit the wild type enzyme. These data suggest that the cysteine is not required for enzyme activity but that the binding of certain metals to that amino acid block DNA incision by either preventing a conformational change in the enzyme after it has bound to a pyrimidine dimer or sterically interfering with the active site residue's accessibility to the pyrimidine dimer

Apurinic/apyrimidinic endonucleases of Mycobacterium tuberculosis protect against DNA damage but are dispensable for the growth of the pathogen in guinea pigs.

Science.gov (United States)

Puri, Rupangi Verma; Reddy, P Vineel; Tyagi, Anil K

2014-01-01

In host cells, Mycobacterium tuberculosis encounters an array of reactive molecules capable of damaging its genome. Non-bulky DNA lesions are the most common damages produced on the exposure of the pathogen to reactive species and base excision repair (BER) pathway is involved in the repair of such damage. During BER, apurinic/apyrimidinic (AP) endonuclease enzymes repair the abasic sites that are generated after spontaneous DNA base loss or by the action of DNA glycosylases, which if left unrepaired lead to inhibition of replication and transcription. However, the role of AP endonucleases in imparting protection against DNA damage and in the growth and pathogenesis of M.tuberculosis has not yet been elucidated. To demonstrate the biological significance of these enzymes in M.tuberculosis, it would be desirable to disrupt the relevant genes and evaluate the resulting mutants for their ability to grow in the host and cause disease. In this study, we have generated M.tuberculosis mutants of the base excision repair (BER) system, disrupted in either one (MtbΔend or MtbΔxthA) or both the AP endonucleases (MtbΔendΔxthA). We demonstrate that these genes are crucial for bacteria to withstand alkylation and oxidative stress in vitro. In addition, the mutant disrupted in both the AP endonucleases (MtbΔendΔxthA) exhibited a significant reduction in its ability to survive inside human macrophages. However, infection of guinea pigs with either MtbΔend or MtbΔxthA or MtbΔendΔxthA resulted in the similar bacillary load and pathological damage in the organs as observed in the case of infection with wild-type M.tuberculosis. The implications of these observations are discussed.

Apurinic/apyrimidinic endonucleases of Mycobacterium tuberculosis protect against DNA damage but are dispensable for the growth of the pathogen in guinea pigs.

Directory of Open Access Journals (Sweden)

Rupangi Verma Puri

Full Text Available In host cells, Mycobacterium tuberculosis encounters an array of reactive molecules capable of damaging its genome. Non-bulky DNA lesions are the most common damages produced on the exposure of the pathogen to reactive species and base excision repair (BER pathway is involved in the repair of such damage. During BER, apurinic/apyrimidinic (AP endonuclease enzymes repair the abasic sites that are generated after spontaneous DNA base loss or by the action of DNA glycosylases, which if left unrepaired lead to inhibition of replication and transcription. However, the role of AP endonucleases in imparting protection against DNA damage and in the growth and pathogenesis of M.tuberculosis has not yet been elucidated. To demonstrate the biological significance of these enzymes in M.tuberculosis, it would be desirable to disrupt the relevant genes and evaluate the resulting mutants for their ability to grow in the host and cause disease. In this study, we have generated M.tuberculosis mutants of the base excision repair (BER system, disrupted in either one (MtbΔend or MtbΔxthA or both the AP endonucleases (MtbΔendΔxthA. We demonstrate that these genes are crucial for bacteria to withstand alkylation and oxidative stress in vitro. In addition, the mutant disrupted in both the AP endonucleases (MtbΔendΔxthA exhibited a significant reduction in its ability to survive inside human macrophages. However, infection of guinea pigs with either MtbΔend or MtbΔxthA or MtbΔendΔxthA resulted in the similar bacillary load and pathological damage in the organs as observed in the case of infection with wild-type M.tuberculosis. The implications of these observations are discussed.

A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease

Science.gov (United States)

The Cas9 endonuclease of the Type II-a clustered regularly interspersed short palindromic repeats (CRISPR), of Streptococcus pyogenes (SpCas9) has been adapted as a widely used tool for genome editing and genome engineering. Herein, we describe a gene encoding a novel Cas9 ortholog (BpsuCas9) and th...

Charge Asymmetric Cosmic Rays as a probe of Flavor Violating Asymmetric Dark Matter

DEFF Research Database (Denmark)

Masina, Isabella; Sannino, Francesco

2011-01-01

The recently introduced cosmic sum rules combine the data from PAMELA and Fermi-LAT cosmic ray experiments in a way that permits to neatly investigate whether the experimentally observed lepton excesses violate charge symmetry. One can in a simple way determine universal properties of the unknown...... component of the cosmic rays. Here we attribute a potential charge asymmetry to the dark sector. In particular we provide models of asymmetric dark matter able to produce charge asymmetric cosmic rays. We consider spin zero, spin one and spin one-half decaying dark matter candidates. We show that lepton...... flavor violation and asymmetric dark matter are both required to have a charge asymmetry in the cosmic ray lepton excesses. Therefore, an experimental evidence of charge asymmetry in the cosmic ray lepton excesses implies that dark matter is asymmetric....

Regulating Effect of Asymmetrical Impeller on the Flow Distributions of Double-sided Centrifugal Compressor

Science.gov (United States)

Yang, Ce; Liu, Yixiong; Yang, Dengfeng; Wang, Benjiang

2017-11-01

To achieve the rebalance of flow distributions of double-sided impellers, a method of improving the radius of rear impeller is presented in this paper. It is found that the flow distributions of front and rear impeller can be adjusted effectively by increasing the radius of rear impeller, thus improves the balance of flow distributions of front and rear impeller. Meanwhile, the working conversion mode process of double-sided centrifugal compressor is also changed. Further analysis shows that the flowrates of blade channels in front impeller are mainly influenced by the circumferential distributions of static pressure in the volute. But the flowrates of rear impeller blade channels are influenced by the outlet flow field of bent duct besides the effects of static pressure distributions in the volute. In the airflow interaction area downstream, the flowrate of blade channel is obviously smaller. By increasing the radius of rear impeller, the work capacity of rear impeller is enhanced, the working mode conversion process from parallel working mode of double-sided impeller to the single impeller working mode is delayed, and the stable working range of double-sided compressor is broadened.

Critical behavior near the Mott transition in the half-filled asymmetric Hubbard model

Energy Technology Data Exchange (ETDEWEB)

Hoang, Anh-Tuan, E-mail: hatuan@iop.vast.ac.vn [Institute of Physics, Vietnam Academy of Science and Technology, Hanoi (Viet Nam); Le, Duc-Anh [Faculty of Physics, Hanoi National University of Education, Xuan Thuy 136, Cau Giay, Hanoi 10000 (Viet Nam)

2016-03-15

We study the half-filled asymmetric Hubbard model within the two-site dynamical mean field theory. At zero temperature, explicit expressions of the critical interaction U{sub c} for the Mott transition and the local self-energy are analytically derived. Critical behavior of the quasiparticle weights and the double occupancy are obtained analytically as functions of the on-site interaction U and the hopping asymmetry r. Our results are in good agreement with the ones obtained by much more sophisticated theory.

Analysis of Endonuclease R·EcoRI Fragments of DNA from Lambdoid Bacteriophages and Other Viruses by Agarose-Gel Electrophoresis

Science.gov (United States)

Helling, Robert B.; Goodman, Howard M.; Boyer, Herbert W.

1974-01-01

By means of agarose-gel electrophoresis, endonuclease R·EcoRI-generated fragments of DNA from various viruses were separated, their molecular weights were determined, and complete or partial fragment maps for lambda, φ80, and hybrid phages were constructed. Images PMID:4372397

Asymmetric electroresistance of cluster glass state in manganites

KAUST Repository

Lourembam, James

2014-03-31

We report the electrostatic modulation of transport in strained Pr0.65(Ca0.75Sr0.25)0.35MnO3 thin films grown on SrTiO3 by gating with ionic liquid in electric double layer transistors (EDLT). In such manganite films with strong phase separation, a cluster glass magnetic state emerges at low temperatures with a spin freezing temperature of about 99 K, which is accompanied by the reentrant insulating state with high resistance below 30 K. In the EDLT, we observe bipolar and asymmetric modulation of the channel resistance, as well as an enhanced electroresistance up to 200% at positive gate bias. Our results provide insights on the carrier-density-dependent correlated electron physics of cluster glass systems.

Cyclodextrins in Asymmetric and Stereospecific Synthesis

Directory of Open Access Journals (Sweden)

Fliur Macaev

2015-09-01

Full Text Available Since their discovery, cyclodextrins have widely been used as green and easily available alternatives to promoters or catalysts of different chemical reactions in water. This review covers the research and application of cyclodextrins and their derivatives in asymmetric and stereospecific syntheses, with their division into three main groups: (1 cyclodextrins promoting asymmetric and stereospecific catalysis in water; (2 cyclodextrins’ complexes with transition metals as asymmetric and stereospecific catalysts; and (3 cyclodextrins’ non-metallic derivatives as asymmetric and stereospecific catalysts. The scope of this review is to systematize existing information on the contribution of cyclodextrins to asymmetric and stereospecific synthesis and, thus, to facilitate further development in this direction.

Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics

DEFF Research Database (Denmark)

Molina, Rafael; Besker, Neva; Marcaida, Maria Jose

2016-01-01

. The cleavage mechanism was related both to key structural effects, such as the position of water molecules and ions participating in the cleavage reaction, and to dynamical effects related to protein behavior. In particular, we found that the protein perturbation pattern significantly changes between cleaved......Homing endonucleases, such as I-DmoI, specifically recognize and cleave long DNA target sequences (∼20 bp) and are potentially powerful tools for genome manipulation. However, inefficient and off-target DNA cleavage seriously limits specific editing in complex genomes. One approach to overcome...

Principles of asymmetric synthesis

CERN Document Server

Gawley, Robert E; Aube, Jeffrey

2012-01-01

The world is chiral. Most of the molecules in it are chiral, and asymmetric synthesis is an important means by which enantiopure chiral molecules may be obtained for study and sale. Using examples from the literature of asymmetric synthesis, this book presents a detailed analysis of the factors that govern stereoselectivity in organic reactions. After an explanation of the basic physical-organic principles governing stereoselective reactions, the authors provide a detailed, annotated glossary of stereochemical terms. A chapter on "Practical Aspects of Asymmetric Synthesis" provides a critical overview of the most common methods for the preparation of enantiomerically pure compounds, techniques for analysis of stereoisomers using chromatographic, spectroscopic, and chiroptical methods. The authors then present an overview of the most important methods in contemporary asymmetric synthesis organized by reaction type. Thus, there are four chapters on carbon-carbon bond forming reactions, one chapter on reductions...

Comparison of light and x-ray sensitometric responses of double-emulsion films for different processing conditions

International Nuclear Information System (INIS)

Blendl, Christian; Buhr, Egbert

2001-01-01

The effects of different film processing conditions on light and x-ray sensitometric responses were compared for a variety of double-emulsion x-ray films. The processing conditions were altered by changes of the developer temperature. Three different exposure variants were applied: x-ray sensitometry using two stepped neutral density attenuators between film and screens, simultaneous double-sided light sensitometry, and single-sided light sensitometry. 13 different types of double-emulsion x-ray films were investigated, among them three asymmetric films. In the special case of exposing the asymmetric films with the single-sided light sensitometer, a method was investigated where each side of the film is exposed at different locations and the sum effect is analyzed. From each sensitometric curve shape two parameters, the logarithmic speed (log S) and the average gradient (G), were evaluated. The results of this study can be summarized as follows: (1) Single-sided and double-sided light sensitometers revealed almost equal changes of log S when the processing conditions are altered. Thus, single-sided light sensitometers can serve as a substitute for double-sided light sensitometers provided that suited exposure methods are used and appropriate sensitometric parameters are evaluated. (2) Light sensitometry quantitatively indicated changes of the film processing that affect the x-ray speed. Hence, light sensitometry is a useful method to monitor changes in film processing

Synthesis method of asymmetric gold particles.

Science.gov (United States)

Jun, Bong-Hyun; Murata, Michael; Hahm, Eunil; Lee, Luke P

2017-06-07

Asymmetric particles can exhibit unique properties. However, reported synthesis methods for asymmetric particles hinder their application because these methods have a limited scale and lack the ability to afford particles of varied shapes. Herein, we report a novel synthetic method which has the potential to produce large quantities of asymmetric particles. Asymmetric rose-shaped gold particles were fabricated as a proof of concept experiment. First, silica nanoparticles (NPs) were bound to a hydrophobic micro-sized polymer containing 2-chlorotritylchloride linkers (2-CTC resin). Then, half-planar gold particles with rose-shaped and polyhedral structures were prepared on the silica particles on the 2-CTC resin. Particle size was controlled by the concentration of the gold source. The asymmetric particles were easily cleaved from the resin without aggregation. We confirmed that gold was grown on the silica NPs. This facile method for synthesizing asymmetric particles has great potential for materials science.

Microinjection of Micrococcus luteus UV-endonuclease restores UV-induced unscheduled DNA synthesis in cells of 9 xeroderma pigmentosum complementation groups.

NARCIS (Netherlands)

A.J.R. de Jonge; W. Vermeulen (Wim); W. Keijzer; J.H.J. Hoeijmakers (Jan); D. Bootsma (Dirk)

1985-01-01

textabstractThe UV-induced unscheduled DNA synthesis (UDS) in cultured cells of excision-deficient xeroderma pigmentosum (XP) complementation groups A through I was assayed after injection of Micrococcus luteus UV-endonuclease using glass microneedles. In all complementation groups a restoration of

Granulomatous colitis: findings on double contrast barium enema and follow-up studies

International Nuclear Information System (INIS)

Song, Jong Gi; Han, Joon Koo; Kim, Seung Hoon; Choo, Sung Wook; Kim, Seung Cheol; Choi, Byung Ihn

1995-01-01

To evaluate the radiologic findings of granulomatous colitis on double contrast barium enema and changes on follow-up studies. Serial double contrast barium enema of six patients with granulomatous colitis confirmed by endoscopic biopsy were reviewed. We analyzed the radiologic findings and their follow-up changes, including aphthous ulcers, lymphoid hyperplasia, deep ulcers, cobble stone appearance, geographic ulcers, asymmetric involvement of ulcers, skip lesions, sinus tract, fistula formation, pseudosacculation, focal stricture, and small bowel involvement. Pretreatment double contrast barium enema findings were aphthous ulcers in five patients, deep ulcer in six, cobble stone appearance in five, longitudinal geographic ulcers in two, fistulas in one, pseudosacculations in two, focal stricture in one, and pseudopolyps in six. Also, anal ulcers were observed in two patients, asymmetric involvement of ulcers in three, skip lesions in four, and small bowel involvement in five in five patients proved to have inactive disease after treatment, aphthous ulcers and deep ulcers disappeared. Geographic ulcers of two patients and anal ulcer of one patients decreased in size or depth. Pseudosacculation in one patient disappeared. Pseudopolyps decreased in two patients, increased in one, and decreased after increase in two. One patient whose disease remained active after treatment showed maintenance or increase of ulcers or fistula. And their pseudosacculation or focal stricture unchanged and pseudopolyps decreased. The major radiologic findings of chronic granulomatous colitis on double contrast barium enema are aphthous ulcer, deep ulcer, cobble stone appearance, discontinuity of the lesion and coexistence of ulcers and pseudopolyps. And, double contrast barium enema is good follow-up modality because its findings correlate with clinical course of the granulomatous colitis after treatment

Spectrophotometric, colorimetric and visually detection of Pseudomonas aeruginosa ETA gene based gold nanoparticles DNA probe and endonuclease enzyme

Science.gov (United States)

Amini, Bahram; Kamali, Mehdi; Salouti, Mojtaba; Yaghmaei, Parichehreh

2018-06-01

Colorimetric DNA detection is preferred over other methods for clinical molecular diagnosis because it does not require expensive equipment. In the present study, the colorimetric method based on gold nanoparticles (GNPs) and endonuclease enzyme was used for the detection of P. aeruginosa ETA gene. Firstly, the primers and probe for P. aeruginosa exotoxin A (ETA) gene were designed and checked for specificity by the PCR method. Then, GNPs were synthesized using the citrate reduction method and conjugated with the prepared probe to develop the new nano-biosensor. Next, the extracted target DNA of the bacteria was added to GNP-probe complex to check its efficacy for P. aeruginosa ETA gene diagnosis. A decrease in absorbance was seen when GNP-probe-target DNA cleaved into the small fragments of BamHI endonuclease due to the weakened electrostatic interaction between GNPs and the shortened DNA. The right shift of the absorbance peak from 530 to 562 nm occurred after adding the endonuclease. It was measured using a UV-VIS absorption spectroscopy that indicates the existence of the P. aeruginosa ETA gene. Sensitivity was determined in the presence of different concentrations of target DNA of P. aeruginosa. The results obtained from the optimized conditions showed that the absorbance value has linear correlation with concentration of target DNA (R: 0.9850) in the range of 10-50 ng mL-1 with the limit detection of 9.899 ng mL-1. Thus, the specificity of the new method for detection of P. aeruginosa was established in comparison with other bacteria. Additionally, the designed assay was quantitatively applied to detect the P. aeruginosa ETA gene from 103 to 108 CFU mL-1 in real samples with a detection limit of 320 CFU mL-1.

Specificity of binding to four-way junctions in DNA by bacteriophage T7 endonuclease I.

OpenAIRE

Parsons, C A; West, S C

1990-01-01

T7 endonuclease I binds specifically to four-way junctions in duplex DNA and promotes their resolution into linear duplexes. Under conditions in which the nuclease activity is blocked by the absence of divalent cations, the enzyme forms a distinct protein-DNA complex with the junction, as detected by gel retardation and filter binding assays. The formation of this complex is structure-specific and contrasts with the short-lived binding complexes formed on linear duplex DNA. The binding comple...

Altered endoribonuclease activity of apurinic/apyrimidinic endonuclease 1 variants identified in the human population.

Directory of Open Access Journals (Sweden)

Wan Cheol Kim

Full Text Available Apurinic/apyrimidinic endonuclease 1 (APE1 is the major mammalian enzyme in the DNA base excision repair pathway and cleaves the DNA phosphodiester backbone immediately 5' to abasic sites. APE1 also has 3'-5' DNA exonuclease and 3' DNA phosphodiesterase activities, and regulates transcription factor DNA binding through its redox regulatory function. The human APE1 has recently been shown to endonucleolytically cleave single-stranded regions of RNA. Towards understanding the biological significance of the endoribonuclease activity of APE1, we examined eight different amino acid substitution variants of APE1 previously identified in the human population. Our study shows that six APE1 variants, D148E, Q51H, I64V, G241R, R237A, and G306A, exhibit a 76-85% reduction in endoribonuclease activity against a specific coding region of the c-myc RNA, yet fully retain the ability to cleave apurinic/apyrimidinic DNA. We found that two APE1 variants, L104R and E126D, exhibit a unique RNase inhibitor-resistant endoribonuclease activity, where the proteins cleave c-myc RNA 3' of specific single-stranded guanosine residues. Expression of L104R and E126D APE1 variants in bacterial Origami cells leads to a 60-80% reduction in colony formation and a 1.5-fold increase in cell doubling time, whereas the other variants, which exhibit diminished endoribonuclease activity, had no effect. These data indicate that two human APE1 variants exhibit a unique endoribonuclease activity, which correlates with their ability to induce cytotoxicity or slow down growth in bacterial cells and supports the notion of their biological functionality.

An ultra-sensitive colorimetric Hg(2+)-sensing assay based on DNAzyme-modified Au NP aggregation, MNPs and an endonuclease.

Science.gov (United States)

Li, Chao; Dai, Peiqing; Rao, Xinyi; Shao, Lin; Cheng, Guifang; He, Pingang; Fang, Yuzhi

2015-01-01

This paper reports the development of an ultra-sensitive colorimetric method for the detection of trace mercury ions involving DNAzymes, Au nanoparticle aggregation, magnetic nanoparticles and an endonuclease. DNAzyme-sensing elements are conjugated to the surface of Au nanoparticle-2, which can crosslink with the T-rich strands coated on Au nanoparticle-1 to form Au nanoparticle aggregation. Other T-rich stands are immobilized on the surface of MNPs. The specific hybridization of these two T-rich strands depends on the presence of Hg(2+), resulting in the formation of a T-Hg(2+)-T structure. Added endonuclease then digests the hybridized strands, and DNAzyme-modified Au NP aggregation is released, catalysing the conversion of the colourless ABTS into a blue-green product by H2O2-mediated oxidation. The increase in the adsorption spectrum of ABTS(+) at 421 nm is related to the concentration of Hg(2+). This assay was validated by detecting mercury ion concentrations in river water. The colorimetric responses were not significantly altered in the presence of 100-fold excesses of other metal ions such as Zn(2+), Pb(2+), Cd(2+), Mn(2+), Ca(2+) and Ni(2+). The inclusion of both Au NP aggregation and an endonuclease enables the assay to eliminate interference from the magnetic nanoparticles with colorimetric detection, decrease the background and improve the detection sensitivity. The calibration curve of the assay was linear over the range of Hg(2+) concentrations from 1 to 30 nM, and the detection limit was 0.8 nM, which is far lower than the 10 nM US EPA limit for drinking water. Copyright © 2014 Elsevier B.V. All rights reserved.

Restoration of ultraviolet-induced unscheduled DNA synthesis of xeroderma pigmentosum cells by the concomitant treatment with bacteriophage T4 endonuclease V and HVJ (Sendai virus)

International Nuclear Information System (INIS)

Tanaka, K.; Sekiguchi, M.; Okada, Y.

1975-01-01

Ultraviolet (uv)-induced unscheduled DNA synthesis of xeroderma pigmentosum cells, belonging to complementation groups, A, B, C, D, and E, was restored to the normal level by concomitant treatment of the cells with T4 endonuclease V and uv-inactivated HVJ (Sendai virus). The present results suggest that T4 endonuclease molecules were inserted effectively into the cells by the interaction of HVJ with the cell membranes, the enzyme was functional on human chromosomal DNA which had been damaged by uv irradiation in the viable cells, all the studied groups of xeroderma pigmentosum (variant was not tested) were defective in the first step (incision) of excision repair

A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations.

Science.gov (United States)

Comeron, Josep M; Reed, Jordan; Christie, Matthew; Jacobs, Julia S; Dierdorff, Jason; Eberl, Daniel F; Manak, J Robert

2016-04-05

Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs), point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array)) pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs) as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1) genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2) identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3) screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv) gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation.

Asymmetric Evolutionary Games

Science.gov (United States)

McAvoy, Alex; Hauert, Christoph

2015-01-01

Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner’s Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

Asymmetrical field emitter

Science.gov (United States)

Fleming, J.G.; Smith, B.K.

1995-10-10

A method is disclosed for providing a field emitter with an asymmetrical emitter structure having a very sharp tip in close proximity to its gate. One preferred embodiment of the present invention includes an asymmetrical emitter and a gate. The emitter having a tip and a side is coupled to a substrate. The gate is connected to a step in the substrate. The step has a top surface and a side wall that is substantially parallel to the side of the emitter. The tip of the emitter is in close proximity to the gate. The emitter is at an emitter potential, and the gate is at a gate potential such that with the two potentials at appropriate values, electrons are emitted from the emitter. In one embodiment, the gate is separated from the emitter by an oxide layer, and the emitter is etched anisotropically to form its tip and its asymmetrical structure. 17 figs.

Rectified motion in an asymmetrically structured channel due to induced-charge electrokinetic and thermo-kinetic phenomena

International Nuclear Information System (INIS)

Sugioka, Hideyuki

2016-01-01

It would be advantageous to move fluid by the gradient of random thermal noises that are omnipresent in the natural world. To achieve this motion, we propose a rectifier that uses a thermal noise along with induced-charge electroosmosis and electrophoresis (ICEO and ICEP) around a metal post cylinder in an asymmetrically structured channel and numerically examine its rectification performance. By the boundary element method combined with the thin double layer approximation, we find that rectified motion occurs in the asymmetrically structured channel due to ICEO and ICEP. Further, by thermodynamical and equivalent circuit methods, we discuss a thermal voltage that drives a rectifier consisting of a fluidic channel of an electrolyte and an impedance as a noise source. Our calculations show that fluid can be moved in the asymmetrically structured channel by the fluctuation of electric fields due to a thermal noise only when there is a temperature difference. In addition, our simple noise argument provides a different perspective for the thermo-kinetic phenomena (around a metal post) which was predicted based on the electrolyte Seebeck effect in our previous paper [H. Sugioka, “Nonlinear thermokinetic phenomena due to the Seebeck effect,” Langmuir 30, 8621 (2014)

Rectified motion in an asymmetrically structured channel due to induced-charge electrokinetic and thermo-kinetic phenomena

Energy Technology Data Exchange (ETDEWEB)

Sugioka, Hideyuki, E-mail: hsugioka@shinshu-u.ac.jp [Frontier Research Center, Canon Inc. 30-2, Shimomaruko 3-chome, Ohta-ku, Tokyo 146-8501, Japan and Department of Mechanical Systems Engineering, Shinshu University 4-17-1 Wakasato, Nagano 380-8553 (Japan)

2016-02-15

It would be advantageous to move fluid by the gradient of random thermal noises that are omnipresent in the natural world. To achieve this motion, we propose a rectifier that uses a thermal noise along with induced-charge electroosmosis and electrophoresis (ICEO and ICEP) around a metal post cylinder in an asymmetrically structured channel and numerically examine its rectification performance. By the boundary element method combined with the thin double layer approximation, we find that rectified motion occurs in the asymmetrically structured channel due to ICEO and ICEP. Further, by thermodynamical and equivalent circuit methods, we discuss a thermal voltage that drives a rectifier consisting of a fluidic channel of an electrolyte and an impedance as a noise source. Our calculations show that fluid can be moved in the asymmetrically structured channel by the fluctuation of electric fields due to a thermal noise only when there is a temperature difference. In addition, our simple noise argument provides a different perspective for the thermo-kinetic phenomena (around a metal post) which was predicted based on the electrolyte Seebeck effect in our previous paper [H. Sugioka, “Nonlinear thermokinetic phenomena due to the Seebeck effect,” Langmuir 30, 8621 (2014)].

Effects of Pioglitazone on Asymmetric Dimethylarginine and Components of the Metabolic Syndrome in Nondiabetic Patients (EPICAMP Study: A Double-Blind, Randomized Clinical Trial

Directory of Open Access Journals (Sweden)

Pedram Shokouh

2013-01-01

Full Text Available The present trial aimed to investigate the effects of pioglitazone on the serum level of asymmetric dimethylarginine (ADMA, a marker of endothelial function, and some indices of inflammation and glucose and lipid metabolism in nondiabetic metabolic syndrome patients. 104 eligible participants (57% female; age between 20 and 70 were enrolled in a double-blind placebo-controlled trial and were randomized to receive either pioglitazone (uptitrated to 30 mg/day or matching placebo for 24 weeks. Participants were clinically examined and a blood sample was obtained at baseline and at the end of the trial. Pioglitazone significantly improved C-reactive protein level irrespective of changes in insulin sensitivity. Compared with the placebo group, alanine and aspartate transaminases were decreased and high-density lipoprotein cholesterol was increased after treatment with pioglitazone. A considerably greater weight gain was also recorded in the intervention group. We failed to observe any significant changes in serum ADMA in either group and between groups with and without adjustment for age, sex, and components of the metabolic syndrome. In a nutshell, pioglitazone seems to have positive effects on lipid profile, liver transaminases, and systemic inflammation. However, its previously demonstrated endothelial function-improving properties do not seem to be mediated by ADMA.

Cinchona alkaloids in asymmetric organocatalysis

NARCIS (Netherlands)

Marcelli, T.; Hiemstra, H.

2010-01-01

This article reviews the applications of cinchona alkaloids as asymmetric catalysts. In the last few years, characterized by the resurgence of interest in asymmetric organocatalysis, cinchona derivatives have been shown to catalyze an outstanding array of chemical reactions, often with remarkable

Design, Generation and Tooth Contact Analysis (TCA) of Asymmetric Face Gear Drive With Modified Geometry

Science.gov (United States)

Litvin, Faydor L.; Fuentes, Alfonso; Hawkins, J. M.; Handschuh, Robert F.

2001-01-01

A new type of face gear drive for application in transmissions, particularly in helicopters, has been developed. The new geometry differs from the existing geometry by application of asymmetric profiles and double-crowned pinion of the face gear mesh. The paper describes the computerized design, simulation of meshing and contact, and stress analysis by finite element method. Special purpose computer codes have been developed to conduct the analysis. The analysis of this new type of face gear is illustrated with a numerical example.

Modeling nanowire and double-gate junctionless field-effect transistors

CERN Document Server

Jazaeri, Farzan

2018-01-01

The first book on the topic, this is a comprehensive introduction to the modeling and design of junctionless field effect transistors (FETs). Beginning with a discussion of the advantages and limitations of the technology, the authors also provide a thorough overview of published analytical models for double-gate and nanowire configurations, before offering a general introduction to the EPFL charge-based model of junctionless FETs. Important features are introduced gradually, including nanowire versus double-gate equivalence, technological design space, junctionless FET performances, short channel effects, transcapacitances, asymmetric operation, thermal noise, interface traps, and the junction FET. Additional features compatible with biosensor applications are also discussed. This is a valuable resource for students and researchers looking to understand more about this new and fast developing field.

Asymmetric quantum-well structures for AlGaN/GaN/AlGaN resonant tunneling diodes

Energy Technology Data Exchange (ETDEWEB)

Yang, Lin' an, E-mail: layang@xidian.edu.cn; Li, Yue; Wang, Ying; Xu, Shengrui; Hao, Yue [State Key Discipline Laboratory of Wide Bandgap Semiconductor Technology, School of Microelectronics, Xidian University, Xi' an 710071 (China)

2016-04-28

Asymmetric quantum-well (QW) structures including the asymmetric potential-barrier and the asymmetric potential-well are proposed for AlGaN/GaN/AlGaN resonant tunneling diodes (RTDs). Theoretical investigation gives that an appropriate decrease in Al composition and thickness for emitter barrier as well as an appropriate increase of both for collector barrier can evidently improve the negative-differential-resistance characteristic of RTD. Numerical simulation shows that RTD with a 1.5-nm-thick GaN well sandwiched by a 1.3-nm-thick Al{sub 0.15}Ga{sub 0.85}N emitter barrier and a 1.7-nm-thick Al{sub 0.25}Ga{sub 0.75}N collector barrier can yield the I-V characteristic having the peak current (Ip) and the peak-to-valley current ratio (PVCR) of 0.39 A and 3.6, respectively, about double that of RTD with a 1.5-nm-thick Al{sub 0.2}Ga{sub 0.8}N for both barriers. It is also found that an introduction of InGaN sub-QW into the diode can change the tunneling mode and achieve higher transmission coefficient of electron. The simulation demonstrates that RTD with a 2.8-nm-thick In{sub 0.03}Ga{sub 0.97}N sub-well in front of a 2.0-nm-thick GaN main-well can exhibit the I-V characteristic having Ip and PVCR of 0.07 A and 11.6, about 7 times and double the value of RTD without sub-QW, respectively. The purpose of improving the structure of GaN-based QW is to solve apparent contradiction between the device structure and the device manufacturability of new generation RTDs for sub-millimeter and terahertz applications.

Alternative Asymmetric Stochastic Volatility Models

NARCIS (Netherlands)

M. Asai (Manabu); M.J. McAleer (Michael)

2010-01-01

textabstractThe stochastic volatility model usually incorporates asymmetric effects by introducing the negative correlation between the innovations in returns and volatility. In this paper, we propose a new asymmetric stochastic volatility model, based on the leverage and size effects. The model is

Multistable wireless micro-actuator based on antagonistic pre-shaped double beams

International Nuclear Information System (INIS)

Liu, X; Lamarque, F; Doré, E; Pouille, P

2015-01-01

This paper presents a monolithic multistable micro-actuator based on antagonistic pre-shaped double beams. The designed micro-actuator is formed by two rows of bistable micro-actuators providing four stable positions. The bistable mechanism for each row is a pair of antagonistic pre-shaped beams. This bistable mechanism has an easier pre-load operation compared to the pre-compressed bistable beams method. Furthermore, it solves the asymmetrical force output problem of parallel pre-shaped bistable double beams. At the same time, the geometrical limit is lower than parallel pre-shaped bistable double beams, which ensures a smaller stroke of the micro-actuator with the same dimensions. The designed micro-actuator is fabricated using laser cutting machine on medium density fiberboard (MDF). The bistability and merits of antagonistic pre-shaped double beams are experimentally validated. Finally, a contactless actuation test is performed using 660 nm wavelength laser heating shape memory alloy (SMA) active elements. (paper)

Multistable wireless micro-actuator based on antagonistic pre-shaped double beams

Science.gov (United States)

Liu, X.; Lamarque, F.; Doré, E.; Pouille, P.

2015-07-01

This paper presents a monolithic multistable micro-actuator based on antagonistic pre-shaped double beams. The designed micro-actuator is formed by two rows of bistable micro-actuators providing four stable positions. The bistable mechanism for each row is a pair of antagonistic pre-shaped beams. This bistable mechanism has an easier pre-load operation compared to the pre-compressed bistable beams method. Furthermore, it solves the asymmetrical force output problem of parallel pre-shaped bistable double beams. At the same time, the geometrical limit is lower than parallel pre-shaped bistable double beams, which ensures a smaller stroke of the micro-actuator with the same dimensions. The designed micro-actuator is fabricated using laser cutting machine on medium density fiberboard (MDF). The bistability and merits of antagonistic pre-shaped double beams are experimentally validated. Finally, a contactless actuation test is performed using 660 nm wavelength laser heating shape memory alloy (SMA) active elements.

Asymmetric ion trap

Science.gov (United States)

Barlow, Stephan E.; Alexander, Michael L.; Follansbee, James C.

1997-01-01

An ion trap having two end cap electrodes disposed asymmetrically about a center of a ring electrode. The inner surface of the end cap electrodes are conformed to an asymmetric pair of equipotential lines of the harmonic formed by the application of voltages to the electrodes. The asymmetry of the end cap electrodes allows ejection of charged species through the closer of the two electrodes which in turn allows for simultaneously detecting anions and cations expelled from the ion trap through the use of two detectors charged with opposite polarity.

An Arginine Finger Regulates the Sequential Action of Asymmetrical Hexameric ATPase in the Double-Stranded DNA Translocation Motor.

Science.gov (United States)

Zhao, Zhengyi; De-Donatis, Gian Marco; Schwartz, Chad; Fang, Huaming; Li, Jingyuan; Guo, Peixuan

2016-10-01

Biological motors are ubiquitous in living systems. Currently, how the motor components coordinate the unidirectional motion is elusive in most cases. Here, we report that the sequential action of the ATPase ring in the DNA packaging motor of bacteriophage ϕ29 is regulated by an arginine finger that extends from one ATPase subunit to the adjacent unit to promote noncovalent dimer formation. Mutation of the arginine finger resulted in the interruption of ATPase oligomerization, ATP binding/hydrolysis, and DNA translocation. Dimer formation reappeared when arginine mutants were mixed with other ATPase subunits that can offer the arginine to promote their interaction. Ultracentrifugation and virion assembly assays indicated that the ATPase was presenting as monomers and dimer mixtures. The isolated dimer alone was inactive in DNA translocation, but the addition of monomer could restore the activity, suggesting that the hexameric ATPase ring contained both dimer and monomers. Moreover, ATP binding or hydrolysis resulted in conformation and entropy changes of the ATPase with high or low DNA affinity. Taking these observations together, we concluded that the arginine finger regulates sequential action of the motor ATPase subunit by promoting the formation of the dimer inside the hexamer. The finding of asymmetrical hexameric organization is supported by structural evidence of many other ATPase systems showing the presence of one noncovalent dimer and four monomer subunits. All of these provide clues for why the asymmetrical hexameric ATPase gp16 of ϕ29 was previously reported as a pentameric configuration by cryo-electron microscopy (cryo-EM) since the contact by the arginine finger renders two adjacent ATPase subunits closer than other subunits. Thus, the asymmetrical hexamer would appear as a pentamer by cryo-EM, a technology that acquires the average of many images. Copyright © 2016 Zhao et al.

Mesoporous Carbon Design for Ionic Liquid-Based, Double-Layer Supercapacitors

OpenAIRE

2010-01-01

Abstract The use of pyrrolidinium-based ionic liquids (ILs) in asymmetric electric double-layer capacitors (AEDLC) with positive and negative carbon electrodes of different weight is a powerful strategy for developing safe, high specific-energy supercapacitors operating at > 3.5 V. The preparation and characterization of ordered (OTC) and disordered (DTC) template carbons, the latter obtained by a fast and low-cost method, are reported. The porosity and capacitance features of the ...

Clinical results and radiographic appearance of the Rashkind double umbrella device in patients with occlusion of the ductus arteriosus

International Nuclear Information System (INIS)

Galal, O.; Sinner, W. von; Azhari, N.; Al-Fadley, F.; De Moor, M.; Boecker, J.; Fawzy, M.E..; Al-Halees, Z.

1997-01-01

Background. The Rashkind double umbrella device for patent arterial duct occlusion has been used in many patients. Its radiographic appearance has not been sufficiently described. Objective. To present the varying radiographic appearances of the Rashkind double umbrella device on the chest X-ray. Materials and methods. The chest radiographs of 69 patients (median age 60 months; median weight 17 kg), who underwent closure of their patent arterial duct between March 1990 and August 1994, were reviewed. The following parameters were evaluated: (1) the size of the heart (cardio-thoracic ratio) and pulmonary vessels, (2) the position of the device in AP/PA and lateral projections. The results of occlusion of the patent arterial duct were also reviewed. Results. Sixty-two of 69 (90 %) pa- tients had complete occlusion after a follow-up between 2 months and 3 1 / 2 years. The cardio-thoracic ratio showed significant reduction at follow-up (P < 0.001). The two different size devices could be well differentiated in the AP and the lateral projection. In 14 patients (20 %) the device was in an asymmetrical position. There was no significant correlation between position of the device and success of occlusion in our material. Conclusion. Complete occlusion of the arterial duct using Rashkind double umbrella devices can be achieved in 90 % of our population. In 20 % the device will have an asymmetrical position. There is no correlation between asymmetrical position of the device in the chest radiograph and residual shunting. (orig.)

Worst Asymmetrical Short-Circuit Current

DEFF Research Database (Denmark)

Arana Aristi, Iván; Holmstrøm, O; Grastrup, L

2010-01-01

In a typical power plant, the production scenario and the short-circuit time were found for the worst asymmetrical short-circuit current. Then, a sensitivity analysis on the missing generator values was realized in order to minimize the uncertainty of the results. Afterward the worst asymmetrical...

Inclined asymmetric librations in exterior resonances

Science.gov (United States)

Voyatzis, G.; Tsiganis, K.; Antoniadou, K. I.

2018-04-01

Librational motion in Celestial Mechanics is generally associated with the existence of stable resonant configurations and signified by the existence of stable periodic solutions and oscillation of critical (resonant) angles. When such an oscillation takes place around a value different than 0 or π , the libration is called asymmetric. In the context of the planar circular restricted three-body problem, asymmetric librations have been identified for the exterior mean motion resonances (MMRs) 1:2, 1:3, etc., as well as for co-orbital motion (1:1). In exterior MMRs the massless body is the outer one. In this paper, we study asymmetric librations in the three-dimensional space. We employ the computational approach of Markellos (Mon Not R Astron Soc 184:273-281, https://doi.org/10.1093/mnras/184.2.273, 1978) and compute families of asymmetric periodic orbits and their stability. Stable asymmetric periodic orbits are surrounded in phase space by domains of initial conditions which correspond to stable evolution and librating resonant angles. Our computations were focused on the spatial circular restricted three-body model of the Sun-Neptune-TNO system (TNO = trans-Neptunian object). We compare our results with numerical integrations of observed TNOs, which reveal that some of them perform 1:2 resonant, inclined asymmetric librations. For the stable 1:2 TNO librators, we find that their libration seems to be related to the vertically stable planar asymmetric orbits of our model, rather than the three-dimensional ones found in the present study.

Asymmetric anode and cathode extraction structure fast recovery diode

Science.gov (United States)

Xie, Jiaqiang; Ma, Li; Gao, Yong

2018-05-01

This paper presents an asymmetric anode structure and cathode extraction fast and soft recovery diode. The device anode is partial-heavily doped and partial-lightly doped. The P+ region is introduced into the cathode. Firstly, the characteristics of the diode are simulated and analyzed. Secondly, the diode was fabricated and its characteristics were tested. The experimental results are in good agreement with the simulation results. The results show that, compared with the P–i–N diode, although the forward conduction characteristic of the diode is declined, the reverse recovery peak current is reduced by 47%, the reverse recovery time is shortened by 20% and the softness factor is doubled. In addition, the breakdown voltage is increased by 10%. Project supported by the National Natural Science Foundation of China (No. 51177133).

Optical precursors with tunneling-induced transparency in asymmetric quantum wells

International Nuclear Information System (INIS)

Peng Yandong; Qi Yihong; Yao Haifeng; Niu Yueping; Gong Shangqing

2011-01-01

A scheme for separating optical precursors from a square-modulated laser pulse through an asymmetric double Al x Ga 1-x As/GaAs quantum-well structure via resonant tunneling is proposed. Destructive interference inhibits linear absorption, and a tunneling-induced transparency (TIT) window appears with normal dispersion, which delays the main pulse; then optical precursors are obtained. Due to resonant tunneling, constructive interference for nonlinear susceptibility is created. The enhanced dispersion in a narrow TIT window is about one order of magnitude larger than that of the linear case. In this case, the main pulse is much delayed and the precursor signals are easier to obtain. Moreover, the main pulse builds up due to the gain introduced by the enhanced cross-nonlinearity.

Reversal modes in asymmetric Ni nanowires

Energy Technology Data Exchange (ETDEWEB)

Leighton, B.; Pereira, A. [Departamento de Fisica, Universidad de Santiago de Chile (USACH), Avda. Ecuador 3493, 917-0124 Santiago (Chile); Escrig, J., E-mail: jescrigm@gmail.com [Departamento de Fisica, Universidad de Santiago de Chile (USACH), Avda. Ecuador 3493, 917-0124 Santiago (Chile); Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Avda. Ecuador 3493, 917-0124 Santiago (Chile)

2012-11-15

We have investigated the evolution of the magnetization reversal mechanism in asymmetric Ni nanowires as a function of their geometry. Circular nanowires are found to reverse their magnetization by the propagation of a vortex domain wall, while in very asymmetric nanowires the reversal is driven by the propagation of a transverse domain wall. The effect of shape asymmetry of the wire on coercivity and remanence is also studied. Angular dependence of the remanence and coercivity is also addressed. Tailoring the magnetization reversal mechanism in asymmetric nanowires can be useful for magnetic logic and race-track memory, both of which are based on the displacement of magnetic domain walls. Finally, an alternative method to detect the presence of magnetic drops is proposed. - Highlights: Black-Right-Pointing-Pointer Asymmetry strongly modifies the magnetic behavior of a wire. Black-Right-Pointing-Pointer Very asymmetric nanowires reverse their magnetization by a transverse domain wall. Black-Right-Pointing-Pointer An alternative method to detect the presence of magnetic drops is proposed. Black-Right-Pointing-Pointer Tailoring the reversal mode in asymmetric nanowires can be useful for potential applications.

In-plane magnetic field-dependent magnetoresistance of gated asymmetric double quantum wells

Czech Academy of Sciences Publication Activity Database

Krupko, Yuriy; Smrčka, Ludvík; Vašek, Petr; Svoboda, Pavel; Cukr, Miroslav; Jansen, L.

2004-01-01

Roč. 22, - (2004), s. 44-47 ISSN 1386-9477. [International Conference on Electronic Properties of Two-Dimensional Systems /15./. Nara, 14.07.2003-18.07.2003] R&D Projects: GA ČR GA202/01/0754 Institutional research plan: CEZ:AV0Z1010914 Keywords : double - layer two-dimensional electron system * magnetotransport * gate voltage Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.898, year: 2004

Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage.

Science.gov (United States)

Brok-Volchanskaya, Vera S; Kadyrov, Farid A; Sivogrivov, Dmitry E; Kolosov, Peter M; Sokolov, Andrey S; Shlyapnikov, Michael G; Kryukov, Valentine M; Granovsky, Igor E

2008-04-01

Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own genes and the flanking sequences by cleaving the recipient DNA. Bacteriophage T4 segB gene, which is located in a cluster of tRNA genes, encodes a protein of unknown function, homologous to homing endonucleases of the GIY-YIG family. We demonstrate that SegB protein is a site-specific endonuclease, which produces mostly 3' 2-nt protruding ends at its DNA cleavage site. Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp sequence. It contains 11-bp conserved sequence, which corresponds to a conserved motif of tRNA TpsiC stem-loop, whereas the remainder of the recognition site is rather degenerate. T4-related phages T2L, RB1 and RB3 contain tRNA gene regions that are homologous to that of phage T4 but lack segB gene and several tRNA genes. In co-infections of phages T4 and T2L, segB gene is inherited with nearly 100% of efficiency. The preferred inheritance depends absolutely on the segB gene integrity and is accompanied by the loss of the T2L tRNA gene region markers. We suggest that SegB is a homing endonuclease that functions to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages.

Asymmetric cryptography based on wavefront sensing.

Science.gov (United States)

Peng, Xiang; Wei, Hengzheng; Zhang, Peng

2006-12-15

A system of asymmetric cryptography based on wavefront sensing (ACWS) is proposed for the first time to our knowledge. One of the most significant features of the asymmetric cryptography is that a trapdoor one-way function is required and constructed by analogy to wavefront sensing, in which the public key may be derived from optical parameters, such as the wavelength or the focal length, while the private key may be obtained from a kind of regular point array. The ciphertext is generated by the encoded wavefront and represented with an irregular array. In such an ACWS system, the encryption key is not identical to the decryption key, which is another important feature of an asymmetric cryptographic system. The processes of asymmetric encryption and decryption are formulized mathematically and demonstrated with a set of numerical experiments.

Quantifying social asymmetric structures.

Science.gov (United States)

Solanas, Antonio; Salafranca, Lluís; Riba, Carles; Sierra, Vicenta; Leiva, David

2006-08-01

Many social phenomena involve a set of dyadic relations among agents whose actions may be dependent. Although individualistic approaches have frequently been applied to analyze social processes, these are not generally concerned with dyadic relations, nor do they deal with dependency. This article describes a mathematical procedure for analyzing dyadic interactions in a social system. The proposed method consists mainly of decomposing asymmetric data into their symmetric and skew-symmetric parts. A quantification of skew symmetry for a social system can be obtained by dividing the norm of the skew-symmetric matrix by the norm of the asymmetric matrix. This calculation makes available to researchers a quantity related to the amount of dyadic reciprocity. With regard to agents, the procedure enables researchers to identify those whose behavior is asymmetric with respect to all agents. It is also possible to derive symmetric measurements among agents and to use multivariate statistical techniques.

Selection of DC voltage magnitude using Fibonacci series for new hybrid asymmetrical multilevel inverter with minimum PIV

Directory of Open Access Journals (Sweden)

M.R. Banaei

2014-09-01

Full Text Available Multilevel inverters are suggested to obtain high quality output voltage. In this paper, a new hybrid configuration is proposed, obtained by cascading one four switches H-bridge cell with a family of multilevel inverters. In addition, by the use of specific sequence for value of DC sources named Fibonacci series, asymmetrical topology of proposed inverter is introduced. Main advantages are that proposed inverter has least Peak Inverse Voltage (PIV than other conventional multilevel converters in both symmetric and asymmetric modes. Also, this topology doubles the number of output levels using only one cascaded four switches H-bridge cell. The PCI-1716 DAQ using PC has been used to generate switching pulses in experimental results. For presenting valid performance of proposed configuration, simulation results carried out by MATLAB/SIMULINK software and the validity of the proposed multilevel inverter is verified by experimental results.

Designing asymmetric multiferroics with strong magnetoelectric coupling

Science.gov (United States)

Lu, Xuezeng; Xiang, Hongjun; Rondinelli, James; Materials Theory; Design Group Team

2015-03-01

Multiferroics offer exciting opportunities for electric-field control of magnetism. Single-phase multiferroics suitable for such applications at room temperature need much more study. Here, we propose the concept of an alternative type of multiferroics, namely, the ``asymmetric multiferroic.'' In asymmetric multiferroics, two locally stable ferroelectric states are not symmetrically equivalent, leading to different magnetic properties between these two states. Furthermore, we predict from first principles that a Fe-Cr-Mo superlattice with the LiNbO3-type structure is such an asymmetric multiferroic. The strong ferrimagnetism, high ferroelectric polarization, and significant dependence of the magnetic transition temperature on polarization make this asymmetric multiferroic an ideal candidate for realizing electric-field control of magnetism at room temperature. Our study suggests that the asymmetric multiferroic may provide an alternative playground for voltage control of magnetism and find its applications in spintronics and quantum computing.

Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae

DEFF Research Database (Denmark)

Haugen, P; Huss, V A; Nielsen, Henrik

1999-01-01

on the complementary strand. A comparison between related group-I introns in the Bangiophyceae revealed homing-endonuclease-like pseudogenes due to frame-shifts and deletions in Porphyra and Bangia. The Scenedesmus and Porphyra introns provide new insights into the evolution and possible novel functions of nuclear...

Clinical results and radiographic appearance of the Rashkind double umbrella device in patients with occlusion of the ductus arteriosus

Energy Technology Data Exchange (ETDEWEB)

Galal, O [King Faisal Specialist Hospital and Research Centre, Riyadh (Saudi Arabia); [Department of Cardiovascular Diseases, MBC 16, King Faisal Specialist Hospital and Research Centre, PO Box 3354, Riyadh 11211 (Saudi Arabia); Sinner, W von; Azhari, N; Al-Fadley, F; De Moor, M; Boecker, J; Fawzy, M E; Al-Halees, Z [King Faisal Specialist Hospital and Research Centre, Riyadh (Saudi Arabia)

1997-12-01

Background. The Rashkind double umbrella device for patent arterial duct occlusion has been used in many patients. Its radiographic appearance has not been sufficiently described. Objective. To present the varying radiographic appearances of the Rashkind double umbrella device on the chest X-ray. Materials and methods. The chest radiographs of 69 patients (median age 60 months; median weight 17 kg), who underwent closure of their patent arterial duct between March 1990 and August 1994, were reviewed. The following parameters were evaluated: (1) the size of the heart (cardio-thoracic ratio) and pulmonary vessels, (2) the position of the device in AP/PA and lateral projections. The results of occlusion of the patent arterial duct were also reviewed. Results. Sixty-two of 69 (90 %) pa- tients had complete occlusion after a follow-up between 2 months and 3{sup 1}/{sub 2} years. The cardio-thoracic ratio showed significant reduction at follow-up (P < 0.001). The two different size devices could be well differentiated in the AP and the lateral projection. In 14 patients (20 %) the device was in an asymmetrical position. There was no significant correlation between position of the device and success of occlusion in our material. Conclusion. Complete occlusion of the arterial duct using Rashkind double umbrella devices can be achieved in 90 % of our population. In 20 % the device will have an asymmetrical position. There is no correlation between asymmetrical position of the device in the chest radiograph and residual shunting. (orig.) With 7 figs., 12 refs.

Molecular characterization of a complex site-specific radiation-induced DNA double-strand break

International Nuclear Information System (INIS)

Datta, K.; Dizdaroglu, M.; Jaruga, P.; Neumann, R.D.; Winters, T.A.

2003-01-01

Radiation lethality is a function of radiation-induced DNA double-strand breaks (DSB). Current models propose the lethality of a DSB to be a function of its structural complexity. We present here for the first time a map of damage associated with a site-specific double-strand break produced by decay of 125 I in a plasmid bound by a 125 I-labeled triplex forming oligonucleotide ( 125 I-TFO). The E. coli DNA repair enzymes, endonuclease IV (endo IV), endonuclease III (endo III), and formamidopyrimidine-DNA glycosylase (Fpg), which recognize AP sites, and pyrimidine and purine base damage respectively, were used as probes in this study. 125 I-TFO bound plasmid was incubated with and without DMSO at -80 deg C for 1 month. No significant difference in DSB yield was observed under these conditions. A 32 base pair fragment from the upstream side of the decay site was isolated by restriction digestion and enzymatically probed to identify damage sites. Endo IV treatment of the 5'-end labeled upper strand indicated clustering of AP sites within 3 bases downstream and 7 bases upstream of the targeted base. Also, repeated experiments consistently detected an AP site 4 bases upstream of the 125 Itarget base. This was further supported by complementary results with the 3'-end labeled upper strand. Endo IV analysis of the lower strand also shows clustering of AP sites near the DSB end. Endo III and Fpg probing demonstrated that base damage is also clustered near the targeted break site. DSBs produced in the absence of DMSO displayed a different pattern of enzyme sensitive damage than those produced in the presence of DMSO. Identification of specific base damage types within the restriction fragment containing the DSB end was achieved with GC/MS. Base damage consisted of 8-hydroguanine, 8-hydroxyadenine, and 5-hydroxycytosine. These lesions were observed at relative yields of 8-hydroguanine and 5-hydroxycytosine to 8-hydroxyadenine of 7.4:1 and 4.7:1, respectively, in the absence

Congenital asymmetric crying face: a case report

Directory of Open Access Journals (Sweden)

Semra Kara

2011-12-01

Full Text Available Congenital asymmetric crying face is an anomalia caused by unilateral absence or weakness of depressor anguli oris muscle The major finding of the disease is the absence or weakness in the outer and lower movement of the commissure during crying. The other expression muscles are normal and the face is symmetric at rest. The asymmetry in congenital asymmetric crying face is most evident during infancy but decreases by age. Congenital asymmetric crying face can be associated with cervicofacial, musclebone, respiratory, genitourinary and central nervous system anomalia. It is diagnosed by physical examination. This paper presents a six days old infant with Congenital asymmetric crying face and discusses the case in terms of diagnosis and disease features.

Apoptotic DNA Degradation into Oligonucleosomal Fragments, but Not Apoptotic Nuclear Morphology, Relies on a Cytosolic Pool of DFF40/CAD Endonuclease*

Science.gov (United States)

Iglesias-Guimarais, Victoria; Gil-Guiñon, Estel; Gabernet, Gisela; García-Belinchón, Mercè; Sánchez-Osuna, María; Casanelles, Elisenda; Comella, Joan X.; Yuste, Victor J.

2012-01-01

Apoptotic cell death is characterized by nuclear fragmentation and oligonucleosomal DNA degradation, mediated by the caspase-dependent specific activation of DFF40/CAD endonuclease. Here, we describe how, upon apoptotic stimuli, SK-N-AS human neuroblastoma-derived cells show apoptotic nuclear morphology without displaying concomitant internucleosomal DNA fragmentation. Cytotoxicity afforded after staurosporine treatment is comparable with that obtained in SH-SY5Y cells, which exhibit a complete apoptotic phenotype. SK-N-AS cell death is a caspase-dependent process that can be impaired by the pan-caspase inhibitor q-VD-OPh. The endogenous inhibitor of DFF40/CAD, ICAD, is correctly processed, and dff40/cad cDNA sequence does not reveal mutations altering its amino acid composition. Biochemical approaches show that both SH-SY5Y and SK-N-AS resting cells express comparable levels of DFF40/CAD. However, the endonuclease is poorly expressed in the cytosolic fraction of healthy SK-N-AS cells. Despite this differential subcellular distribution of DFF40/CAD, we find no differences in the subcellular localization of both pro-caspase-3 and ICAD between the analyzed cell lines. After staurosporine treatment, the preferential processing of ICAD in the cytosolic fraction allows the translocation of DFF40/CAD from this fraction to a chromatin-enriched one. Therefore, the low levels of cytosolic DFF40/CAD detected in SK-N-AS cells determine the absence of DNA laddering after staurosporine treatment. In these cells DFF40/CAD cytosolic levels can be restored by the overexpression of their own endonuclease, which is sufficient to make them proficient at degrading their chromatin into oligonucleosome-size fragments after staurosporine treatment. Altogether, the cytosolic levels of DFF40/CAD are determinants in achieving a complete apoptotic phenotype, including oligonucleosomal DNA degradation. PMID:22253444

Power loss and energy density of the asymmetric ultracapacitor loaded with molybdenum doped manganese oxide

International Nuclear Information System (INIS)

Wang, Yue-Sheng; Tsai, Dah-Shyang; Chung, Wen-Hung; Syu, Yong-Sin; Huang, Ying-Sheng

2012-01-01

Highlights: ► Mo-doping (15 mol%) enhances capacitance and diminishes oxide resistance. ► Influences of Mo-doped MnO 2 are analyzed at the level of capacitor power and energy. ► Polarization loss of the asymmetric capacitor is more than that of the symmetric one. ► Pseudocapacitance benefit on energy is evaluated with power and current densities. - Abstract: Ultracapacitors of asymmetric configuration have been prepared with activated carbon (AC) and undoped or Mo-doped manganese oxide (MnO 2 ) in 1.0 M Na 2 SO 4 electrolyte. Phase analysis shows the AC powder, 1–15 μm in size, contains both disordered and graphitic structures, and the undoped and Mo-doped oxide powder, 0.05–0.20 μm in particle size, mainly involves amorphous MnO 2 and MoO 2 . CV results indicate the single electrode of AC plus 10 wt% Mo-doped MnO 2 (A9O M 1) is superior to the electrode with undoped MnO 2 or high content of doped MnO 2 , exhibiting features of double layer capacitance at high scan rate and pseudocapacitance characteristics at low scan rate. When assembled with a negative electrode of AC, the capacitor of positive A9O M 1 electrode demonstrates the least power loss among three asymmetric capacitors. This asymmetric capacitor also shows a higher capacitance than the symmetric AC capacitor when the current density is less than 8.0 A g −1 in 1.8 V potential window. But a higher electrode resistance of A9O M 1, in contrast with AC, compromises its capacitance plus. When the energy density of A9O M 1 asymmetric capacitor is compared with that of symmetric AC capacitor at the same power level, the capacitance benefit on energy density is restricted to current density ≤ 3.0 A g −1 .

Can double-peaked lines indicate merging effects in AGNs?

Directory of Open Access Journals (Sweden)

Popović L.Č.

2000-01-01

Full Text Available The influence of merging effects in the central part of an Active Galactic Nucleus (AGN on the emission spectral line shapes are discussed. We present a model of close binary Broad Line Region. The numerical experiments show that the merging effects can explain double peaked lines. The merging effects may also be present in the center of AGNs, although they emit slightly asymmetric as well as symmetric and relatively stable (in profile shape spectral lines. Depending on the black hole masses and their orbit elements such model may explain some of the line profile shapes observed in AGNs. This work shows that if one is looking for the merging effects in the central region as well as in the wide field structure of AGNs, he should first pay attention to objects which have double peaked lines.

Theoretical investigations on a class of double-focus planar lens on the anisotropic material

Science.gov (United States)

Bozorgi, Mahdieh; Atlasbaf, Zahra

2017-05-01

We study a double-focus lens constituted of V-shaped plasmonic nano-antennas (VSPNAs) on the anisotropic TiO2 thin film. The phase and amplitude variations of cross-polarized scattered wave from a unit cell are computed by the developed fast Method of Moments (MoM) in which the dyadic Green's function is evaluated with the transmission line model in the spectral domain. Using the calculated phase and amplitude diagrams, a double-focus lens on the anisotropic thin film is designed in 2 μm. To validate the numerical results, the designed lens is analysed using a full-wave EM-solver. The obtained results show a tunable asymmetric behavior in the focusing intensity of the focal spots for different incident polarizations. It is shown that changing the thickness of anisotropic thin film leads to the changing in such an asymmetric behavior and also the intensity ratio of two focal spots. In addition, the lens performance is examined in the broadband wavelength range from 1.76 to 2.86 μm. It is achieved that the increasing the wavelength leads to decreasing the focal distances of the designed lens and increasing its numerical aperture (NA).

Energy capture and storage in asymmetrically multistable modular structures inspired by skeletal muscle

Science.gov (United States)

Kidambi, Narayanan; Harne, Ryan L.; Wang, K. W.

2017-08-01

The remarkable versatility and adaptability of skeletal muscle that arises from the assembly of its nanoscale cross-bridges into micro-scale assemblies known as sarcomeres provides great inspiration for the development of advanced adaptive structures and material systems. Motivated by the capability of cross-bridges to capture elastic strain energy to improve the energetic efficiency of sudden movements and repeated motions, and by models of cross-bridge power stroke motions and sarcomere contractile behaviors that incorporate asymmetric, bistable potential energy landscapes, this research develops and studies modular mechanical structures that trap and store energy in higher-energy configurations. Modules exhibiting tailorable asymmetric bistability are first designed and fabricated, revealing how geometric parameters influence the asymmetry of the resulting double-well energy landscapes. These experimentally-observed characteristics are then investigated with numerical and analytical methods to characterize the dynamics of asymmetrically bistable modules. The assembly of such modules into greater structures generates complex, multi-well energy landscapes with stable system configurations exhibiting different quantities of stored elastic potential energy. Dynamic analyses illustrate the ability of these structures to capture a portion of the initial kinetic energy due to impulsive excitations as recoverable strain potential energy, and reveal how stiffness parameters, damping, and the presence of thermal noise in micro- and nano-scale applications influence energy capture behaviors. The insights gained could foster the development of advanced structural/material systems inspired by skeletal muscle, including actuators that effectively capture, store, and release energy, as well as adaptive, robust, and reusable armors and protective devices.

Dynamic JUNQ inclusion bodies are asymmetrically inherited in mammalian cell lines through the asymmetric partitioning of vimentin.

Science.gov (United States)

Ogrodnik, Mikołaj; Salmonowicz, Hanna; Brown, Rachel; Turkowska, Joanna; Średniawa, Władysław; Pattabiraman, Sundararaghavan; Amen, Triana; Abraham, Ayelet-chen; Eichler, Noam; Lyakhovetsky, Roman; Kaganovich, Daniel

2014-06-03

Aging is associated with the accumulation of several types of damage: in particular, damage to the proteome. Recent work points to a conserved replicative rejuvenation mechanism that works by preventing the inheritance of damaged and misfolded proteins by specific cells during division. Asymmetric inheritance of misfolded and aggregated proteins has been shown in bacteria and yeast, but relatively little evidence exists for a similar mechanism in mammalian cells. Here, we demonstrate, using long-term 4D imaging, that the vimentin intermediate filament establishes mitotic polarity in mammalian cell lines and mediates the asymmetric partitioning of damaged proteins. We show that mammalian JUNQ inclusion bodies containing soluble misfolded proteins are inherited asymmetrically, similarly to JUNQ quality-control inclusions observed in yeast. Mammalian IPOD-like inclusion bodies, meanwhile, are not always inherited by the same cell as the JUNQ. Our study suggests that the mammalian cytoskeleton and intermediate filaments provide the physical scaffold for asymmetric inheritance of dynamic quality-control JUNQ inclusions. Mammalian IPOD inclusions containing amyloidogenic proteins are not partitioned as effectively during mitosis as their counterparts in yeast. These findings provide a valuable mechanistic basis for studying the process of asymmetric inheritance in mammalian cells, including cells potentially undergoing polar divisions, such as differentiating stem cells and cancer cells.

Capacitorless one-transistor dynamic random-access memory based on asymmetric double-gate Ge/GaAs-heterojunction tunneling field-effect transistor with n-doped boosting layer and drain-underlap structure

Science.gov (United States)

Yoon, Young Jun; Seo, Jae Hwa; Kang, In Man

2018-04-01

In this work, we present a capacitorless one-transistor dynamic random-access memory (1T-DRAM) based on an asymmetric double-gate Ge/GaAs-heterojunction tunneling field-effect transistor (TFET) for DRAM applications. The n-doped boosting layer and gate2 drain-underlap structure is employed in the device to obtain an excellent 1T-DRAM performance. The n-doped layer inserted between the source and channel regions improves the sensing margin because of a high rate of increase in the band-to-band tunneling (BTBT) probability. Furthermore, because the gate2 drain-underlap structure reduces the recombination rate that occurs between the gate2 and drain regions, a device with a gate2 drain-underlap length (L G2_D-underlap) of 10 nm exhibited a longer retention performance. As a result, by applying the n-doped layer and gate2 drain-underlap structure, the proposed device exhibited not only a high sensing margin of 1.11 µA/µm but also a long retention time of greater than 100 ms at a temperature of 358 K (85 °C).

Multicatalyst system in asymmetric catalysis

CERN Document Server

Zhou, Jian

2014-01-01

This book introduces multi-catalyst systems by describing their mechanism and advantages in asymmetric catalysis.  Helps organic chemists perform more efficient catalysis with step-by-step methods  Overviews new concepts and progress for greener and economic catalytic reactions  Covers topics of interest in asymmetric catalysis including bifunctional catalysis, cooperative catalysis, multimetallic catalysis, and novel tandem reactions   Has applications for pharmaceuticals, agrochemicals, materials, and flavour and fragrance

Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

Energy Technology Data Exchange (ETDEWEB)

Chen, Chuanying; Beck, Brian W.; Krause, Kurt; Weksberg, Tiffany E.; Pettitt, Bernard M.

2007-02-15

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

Computational study of hydration at the TD damaged site of DNA in complex with repair enzyme T4 endonuclease V

International Nuclear Information System (INIS)

Pinak, Miroslav

2000-02-01

An analysis of the distribution of water around DNA surface focusing on the role of the distribution of water molecules in the proper recognition of damaged site by repair enzyme T4 Endonuclease V was performed. The native DNA dodecamer, dodecamer with the thymine dimer (TD) and complex of DNA and part of repair enzyme T4 Endonuclease V were examined throughout the 500 ps of molecular dynamics simulation. During simulation the number of water molecules close to the DNA atoms and the residence time were calculated. There is an increase in number of water molecules lying in the close vicinity to TD if compared with those lying close to two native thymines (TT). Densely populated area with water molecules around TD is one of the factors detected by enzyme during scanning process. The residence time was found higher for molecule of the complex and the six water molecules were found occupying the stabile positions between the TD and catalytic center close to atoms P, C3' and N3. These molecules originate water mediated hydrogen bond network that contribute to the stability of complex required for the onset of repair process. (author)

Computational study of hydration at the TD damaged site of DNA in complex with repair enzyme T4 endonuclease V

Energy Technology Data Exchange (ETDEWEB)

Pinak, Miroslav [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

2000-02-01

An analysis of the distribution of water around DNA surface focusing on the role of the distribution of water molecules in the proper recognition of damaged site by repair enzyme T4 Endonuclease V was performed. The native DNA dodecamer, dodecamer with the thymine dimer (TD) and complex of DNA and part of repair enzyme T4 Endonuclease V were examined throughout the 500 ps of molecular dynamics simulation. During simulation the number of water molecules close to the DNA atoms and the residence time were calculated. There is an increase in number of water molecules lying in the close vicinity to TD if compared with those lying close to two native thymines (TT). Densely populated area with water molecules around TD is one of the factors detected by enzyme during scanning process. The residence time was found higher for molecule of the complex and the six water molecules were found occupying the stabile positions between the TD and catalytic center close to atoms P, C3' and N3. These molecules originate water mediated hydrogen bond network that contribute to the stability of complex required for the onset of repair process. (author)

Vortex Dynamics of Asymmetric Heave Plates

Science.gov (United States)

Rusch, Curtis; Maurer, Benjamin; Polagye, Brian

2017-11-01

Heave plates can be used to provide reaction forces for wave energy converters, which harness the power in ocean surface waves to produce electricity. Heave plate inertia includes both the static mass of the heave plate, as well as the ``added mass'' of surrounding water accelerated with the object. Heave plate geometries may be symmetric or asymmetric, with interest in asymmetric designs driven by the resulting hydrodynamic asymmetry. Limited flow visualization has been previously conducted on symmetric heave plates, but flow visualization of asymmetric designs is needed to understand the origin of observed hydrodynamic asymmetries and their dependence on the Keulegan-Carpenter number. For example, it is hypothesized that the time-varying added mass of asymmetric heave plates is caused by vortex shedding, which is related to oscillation amplitude. Here, using direct flow visualization, we explore the relationship between vortex dynamics and time-varying added mass and drag. These results suggest potential pathways for more advanced heave plate designs that can exploit vortex formation and shedding to achieve more favorable hydrodynamic properties for wave energy converters.

Small-angle X-ray scattering analysis reveals the ATP-bound monomeric state of the ATPase domain from the homodimeric MutL endonuclease, a GHKL phosphotransferase superfamily protein.

Science.gov (United States)

Iino, Hitoshi; Hikima, Takaaki; Nishida, Yuya; Yamamoto, Masaki; Kuramitsu, Seiki; Fukui, Kenji

2015-05-01

DNA mismatch repair is an excision system that removes mismatched bases chiefly generated by replication errors. In this system, MutL endonucleases direct the excision reaction to the error-containing strand of the duplex by specifically incising the newly synthesized strand. Both bacterial homodimeric and eukaryotic heterodimeric MutL proteins belong to the GHKL ATPase/kinase superfamily that comprises the N-terminal ATPase and C-terminal dimerization regions. Generally, the GHKL proteins show large ATPase cycle-dependent conformational changes, including dimerization-coupled ATP binding of the N-terminal domain. Interestingly, the ATPase domain of human PMS2, a subunit of the MutL heterodimer, binds ATP without dimerization. The monomeric ATP-bound state of the domain has been thought to be characteristic of heterodimeric GHKL proteins. In this study, we characterized the ATP-bound state of the ATPase domain from the Aquifex aeolicus MutL endonuclease, which is a homodimeric GHKL protein unlike the eukaryotic MutL. Gel filtration, dynamic light scattering, and small-angle X-ray scattering analyses clearly showed that the domain binds ATP in a monomeric form despite its homodimeric nature. This indicates that the uncoupling of dimerization and ATP binding is a common feature among bacterial and eukaryotic MutL endonucleases, which we suggest is closely related to the molecular mechanisms underlying mismatch repair.

Renewable resource management under asymmetric information

DEFF Research Database (Denmark)

Jensen, Frank; Andersen, Peder; Nielsen, Max

2013-01-01

Asymmetric information between fishermen and the regulator is important within fisheries. The regulator may have less information about stock sizes, prices, costs, effort, productivity and catches than fishermen. With asymmetric information, a strong analytical tool is principal-agent analysis....... In this paper, we study asymmetric information about productivity within a principal-agent framework and a tax on fishing effort is considered. It is shown that a second best optimum can be achieved if the effort tax is designed such that low-productivity agents rent is exhausted, while high-productivity agents...... receive an information rent. The information rent is equivalent to the total incentive cost. The incentive costs arise as we want to reveal the agent's type....

Subcopula-based measure of asymmetric association for contingency tables.

Science.gov (United States)

Wei, Zheng; Kim, Daeyoung

2017-10-30

For the analysis of a two-way contingency table, a new asymmetric association measure is developed. The proposed method uses the subcopula-based regression between the discrete variables to measure the asymmetric predictive powers of the variables of interest. Unlike the existing measures of asymmetric association, the subcopula-based measure is insensitive to the number of categories in a variable, and thus, the magnitude of the proposed measure can be interpreted as the degree of asymmetric association in the contingency table. The theoretical properties of the proposed subcopula-based asymmetric association measure are investigated. We illustrate the performance and advantages of the proposed measure using simulation studies and real data examples. Copyright © 2017 John Wiley & Sons, Ltd.

Modelling asymmetric growth in crowded plant communities

DEFF Research Database (Denmark)

Damgaard, Christian

2010-01-01

A class of models that may be used to quantify the effect of size-asymmetric competition in crowded plant communities by estimating a community specific degree of size-asymmetric growth for each species in the community is suggested. The model consists of two parts: an individual size......-asymmetric growth part, where growth is assumed to be proportional to a power function of the size of the individual, and a term that reduces the relative growth rate as a decreasing function of the individual plant size and the competitive interactions from other plants in the neighbourhood....

Asymmetric Frontal Brain Activity and Parental Rejection

NARCIS (Netherlands)

Huffmeijer, R.; Alink, L.R.A.; Tops, M.; Bakermans-Kranenburg, M.J.; van IJzendoorn, M.H.

2013-01-01

Asymmetric frontal brain activity has been widely implicated in reactions to emotional stimuli and is thought to reflect individual differences in approach-withdrawal motivation. Here, we investigate whether asymmetric frontal activity, as a measure of approach-withdrawal motivation, also predicts

Asymmetric dominance and asymmetric mate choice oppose premating isolation after allopatric divergence.

Science.gov (United States)

Sefc, Kristina M; Hermann, Caroline M; Steinwender, Bernd; Brindl, Hanna; Zimmermann, Holger; Mattersdorfer, Karin; Postl, Lisbeth; Makasa, Lawrence; Sturmbauer, Christian; Koblmüller, Stephan

2015-04-01

Assortative mating promotes reproductive isolation and allows allopatric speciation processes to continue in secondary contact. As mating patterns are determined by mate preferences and intrasexual competition, we investigated male-male competition and behavioral isolation in simulated secondary contact among allopatric populations. Three allopatric color morphs of the cichlid fish Tropheus were tested against each other. Dyadic male-male contests revealed dominance of red males over bluish and yellow-blotch males. Reproductive isolation in the presence of male-male competition was assessed from genetic parentage in experimental ponds and was highly asymmetric among pairs of color morphs. Red females mated only with red males, whereas the other females performed variable degrees of heteromorphic mating. Discrepancies between mating patterns in ponds and female preferences in a competition-free, two-way choice paradigm suggested that the dominance of red males interfered with positive assortative mating of females of the subordinate morphs and provoked asymmetric hybridization. Between the nonred morphs, a significant excess of negative assortative mating by yellow-blotch females with bluish males did not coincide with asymmetric dominance among males. Hence, both negative assortative mating preferences and interference of male-male competition with positive assortative preferences forestall premating isolation, the latter especially in environments unsupportive of competition-driven spatial segregation.

Method development of damage detection in asymmetric buildings

Science.gov (United States)

Wang, Yi; Thambiratnam, David P.; Chan, Tommy H. T.; Nguyen, Andy

2018-01-01

Aesthetics and functionality requirements have caused most buildings to be asymmetric in recent times. Such buildings exhibit complex vibration characteristics under dynamic loads as there is coupling between the lateral and torsional components of vibration, and are referred to as torsionally coupled buildings. These buildings require three dimensional modelling and analysis. In spite of much recent research and some successful applications of vibration based damage detection methods to civil structures in recent years, the applications to asymmetric buildings has been a challenging task for structural engineers. There has been relatively little research on detecting and locating damage specific to torsionally coupled asymmetric buildings. This paper aims to compare the difference in vibration behaviour between symmetric and asymmetric buildings and then use the vibration characteristics for predicting damage in them. The need for developing a special method to detect damage in asymmetric buildings thus becomes evident. Towards this end, this paper modifies the traditional modal strain energy based damage index by decomposing the mode shapes into their lateral and vertical components and to form component specific damage indices. The improved approach is then developed by combining the modified strain energy based damage indices with the modal flexibility method which was modified to suit three dimensional structures to form a new damage indicator. The procedure is illustrated through numerical studies conducted on three dimensional five-story symmetric and asymmetric frame structures with the same layout, after validating the modelling techniques through experimental testing of a laboratory scale asymmetric building model. Vibration parameters obtained from finite element analysis of the intact and damaged building models are then applied into the proposed algorithms for detecting and locating the single and multiple damages in these buildings. The results

Asymmetric Synthesis via Chiral Aziridines

DEFF Research Database (Denmark)

Tanner, David Ackland; Harden, Adrian; Wyatt, Paul

1996-01-01

A series of chiral bis(aziridines) has been synthesised and evaluated as chelating ligands for a variety of asymmetric transformations mediated by metals [Os (dihydroxylation), Pd (allylic alkylation) Cu (cyclopropanation and aziridination, Li (1,2-addition of organolithiums to imines)]. In the b......A series of chiral bis(aziridines) has been synthesised and evaluated as chelating ligands for a variety of asymmetric transformations mediated by metals [Os (dihydroxylation), Pd (allylic alkylation) Cu (cyclopropanation and aziridination, Li (1,2-addition of organolithiums to imines...

Optimal multicopy asymmetric Gaussian cloning of coherent states

International Nuclear Information System (INIS)

Fiurasek, Jaromir; Cerf, Nicolas J.

2007-01-01

We investigate the asymmetric Gaussian cloning of coherent states which produces M copies from N input replicas in such a way that the fidelity of each copy may be different. We show that the optimal asymmetric Gaussian cloning can be performed with a single phase-insensitive amplifier and an array of beam splitters. We obtain a simple analytical expression characterizing the set of optimal asymmetric Gaussian cloning machines and prove the optimality of these cloners using the formalism of Gaussian completely positive maps and semidefinite programming techniques. We also present an alternative implementation of the asymmetric cloning machine where the phase-insensitive amplifier is replaced with a beam splitter, heterodyne detector, and feedforward

Optimal multicopy asymmetric Gaussian cloning of coherent states

Science.gov (United States)

Fiurášek, Jaromír; Cerf, Nicolas J.

2007-05-01

We investigate the asymmetric Gaussian cloning of coherent states which produces M copies from N input replicas in such a way that the fidelity of each copy may be different. We show that the optimal asymmetric Gaussian cloning can be performed with a single phase-insensitive amplifier and an array of beam splitters. We obtain a simple analytical expression characterizing the set of optimal asymmetric Gaussian cloning machines and prove the optimality of these cloners using the formalism of Gaussian completely positive maps and semidefinite programming techniques. We also present an alternative implementation of the asymmetric cloning machine where the phase-insensitive amplifier is replaced with a beam splitter, heterodyne detector, and feedforward.

Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation. [Haemophilus influenzae, Escherichia coli, Paramecium aurelia

Energy Technology Data Exchange (ETDEWEB)

Lacks, S.; Greenberg, B.

1977-01-01

Restriction endonucleases Dpn I and Dpn II are produced by two distinct strains of Diplococcus pneumoniae. The two enzymes show complementary specificity with respect to methylation of sites in DNA. From the identity of its cleavage site with that of Mbo I, it appears that Dpn II cleaves at the unmodified sequence 5'-G-A-T-C-3'. Dpn I cleaves at the same sequence when the adenine residue is methylated. Both enzymes produce only double-strand breaks in susceptible DNA. Their susceptibility to Dpn I and not Dpn II shows that essentially all the G-A-T-C sequences are methylated in DNA from the pneumococcal strain that produces Dpn II as well as in DNA from Hemophilus influenzae and Escherichia coli. In the dam-3 mutant of E. coli none of these sequences appear to be methylated. Residual adenine methylation in the dam-3 mutant DNA most likely occurs at different sites. Different but characteristic degrees of methylation at G-A-T-C sites are found in the DNA of bacterial viruses grown in E. coli. DNAs from mammalian cells and viruses are not methylated at this sequence. Mitochondrial DNA from Paramecium aurelia is not methylated, but a small proportion of G-A-T-C sequences in the macronuclear DNA of this eukaryote appear to be methylated. Possible roles of sequence-specific methylation in the accommodation of plasmids, in the replication of DNA, in the regulation of gene function and in the restriction of viral infection are discussed.

Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family

Directory of Open Access Journals (Sweden)

Zylicz-Stachula Agnieszka

2009-05-01

Full Text Available Abstract Background Restriction-modification systems are a diverse class of enzymes. They are classified into four major types: I, II, III and IV. We have previously proposed the existence of a Thermus sp. enzyme family, which belongs to type II restriction endonucleases (REases, however, it features also some characteristics of types I and III. Members include related thermophilic endonucleases: TspGWI, TaqII, TspDTI, and Tth111II. Results Here we describe cloning, mutagenesis and analysis of the prototype TspGWI enzyme that recognises the 5'-ACGGA-3' site and cleaves 11/9 nt downstream. We cloned, expressed, and mutagenised the tspgwi gene and investigated the properties of its product, the bifunctional TspGWI restriction/modification enzyme. Since TspGWI does not cleave DNA completely, a cloning method was devised, based on amino acid sequencing of internal proteolytic fragments. The deduced amino acid sequence of the enzyme shares significant sequence similarity with another representative of the Thermus sp. family – TaqII. Interestingly, these enzymes recognise similar, yet different sequences in the DNA. Both enzymes cleave DNA at the same distance, but differ in their ability to cleave single sites and in the requirement of S-adenosylmethionine as an allosteric activator for cleavage. Both the restriction endonuclease (REase and methyltransferase (MTase activities of wild type (wt TspGWI (either recombinant or isolated from Thermus sp. are dependent on the presence of divalent cations. Conclusion TspGWI is a bifunctional protein comprising a tandem arrangement of Type I-like domains; particularly noticeable is the central HsdM-like module comprising a helical domain and a highly conserved S-adenosylmethionine-binding/catalytic MTase domain, containing DPAVGTG and NPPY motifs. TspGWI also possesses an N-terminal PD-(D/EXK nuclease domain related to the corresponding domains in HsdR subunits, but lacks the ATP-dependent translocase module

Double valley Dirac fermions for 3D and 2D Hg$_{1-x}$Cd$_x$Te with strong asymmetry

OpenAIRE

Marchewka, M.

2017-01-01

In this paper the possibility to bring about the double- valley Dirac fermions in some quantum structures is predicted. These quantum structures are: strained 3D Hg$_{1-x}$Cd$_x$Te topological insulator (TI) with strong interface inversion asymmetry and the asymmetric Hg$_{1-x}$Cd$_x$Te double quantum wells (DQW). The numerical analysis of the dispersion relation for 3D TI Hg$_{1-x}$Cd$_x$Te for the proper Cd ($x$)-content of in the Hg$_{1-x}$Cd$_x$Te-compound clearly show that the inversion ...

Modeling Electric Double-Layers Including Chemical Reaction Effects

DEFF Research Database (Denmark)

Paz-Garcia, Juan Manuel; Johannesson, Björn; Ottosen, Lisbeth M.

2014-01-01

A physicochemical and numerical model for the transient formation of an electric double-layer between an electrolyte and a chemically-active flat surface is presented, based on a finite elements integration of the nonlinear Nernst-Planck-Poisson model including chemical reactions. The model works...... for symmetric and asymmetric multi-species electrolytes and is not limited to a range of surface potentials. Numerical simulations are presented, for the case of a CaCO3 electrolyte solution in contact with a surface with rate-controlled protonation/deprotonation reactions. The surface charge and potential...... are determined by the surface reactions, and therefore they depends on the bulk solution composition and concentration...

Lamb wave band gaps in one-dimensional radial phononic crystal plates with periodic double-sided corrugations

Energy Technology Data Exchange (ETDEWEB)

Li, Yinggang [School of Mechanical Engineering and State Key Laboratory for Strength and Vibration of Mechanical Structures, Xi’an Jiaotong University, Xi’an, 710049 (China); School of Transportation, Wuhan University of Technology, Wuhan 430070 (China); Chen, Tianning [School of Mechanical Engineering and State Key Laboratory for Strength and Vibration of Mechanical Structures, Xi’an Jiaotong University, Xi’an, 710049 (China); Wang, Xiaopeng, E-mail: xpwang@mail.xjtu.edu.cn [School of Mechanical Engineering and State Key Laboratory for Strength and Vibration of Mechanical Structures, Xi’an Jiaotong University, Xi’an, 710049 (China); Li, Suobin [School of Mechanical Engineering and State Key Laboratory for Strength and Vibration of Mechanical Structures, Xi’an Jiaotong University, Xi’an, 710049 (China)

2015-11-01

In this paper, we present the theoretical investigation of Lamb wave propagation in one-dimensional radial phononic crystal (RPC) plates with periodic double-sided corrugations. The dispersion relations, the power transmission spectra, and the displacement fields of the eigenmodes are studied by using the finite element method based on two-dimensional axial symmetry models in cylindrical coordinates. Numerical results show that the proposed RPC plates with periodic double-sided corrugations can yield several band gaps with a variable bandwidth for Lamb waves. The formation mechanism of band gaps in the double-sided RPC plates is attributed to the coupling between the Lamb modes and the in-phase and out-phases resonant eigenmodes of the double-sided corrugations. We investigate the evolution of band gaps in the double-sided RPC plates with the corrugation heights on both sides arranged from an asymmetrical distribution to a symmetrical distribution gradually. Significantly, with the introduction of symmetric double-sided corrugations, the antisymmetric Lamb mode is suppressed by the in-phase resonant eigenmodes of the double-sided corrugations, resulting in the disappearance of the lowest band gap. Furthermore, the effects of the geometrical parameters on the band gaps are further explored numerically.

Survey of beta-particle interaction experiments with asymmetric matter

Science.gov (United States)

Van Horn, J. David; Wu, Fei

2018-05-01

Asymmetry is a basic property found at multiple scales in the universe. Asymmetric molecular interactions are fundamental to the operation of biological systems in both signaling and structural roles. Other aspects of asymmetry are observed and useful in many areas of science and engineering, and have been studied since the discovery of chirality in tartrate salts. The observation of parity violation in beta decay provided some impetus for later experiments using asymmetric particles. Here we survey historical work and experiments related to electron (e-) or positron (e+) polarimetry and their interactions with asymmetric materials in gas, liquid and solid forms. Asymmetric interactions may be classified as: 1) stereorecognition, 2) stereoselection and 3) stereoinduction. These three facets of physical stereochemistry are unique but interrelated; and examples from chemistry and materials science illustrate these aspects. Experimental positron and electron interactions with asymmetric materials may be classified in like manner. Thus, a qualitative assessment of helical and polarized positron experiments with different forms of asymmetric matter from the past 40 years is presented, as well as recent experiments with left-hand and right-hand single crystal quartz and organic compounds. The purpose of this classification and review is to evaluate the field for potential new experiments and directions for positron (or electron) studies with asymmetric materials.

Comparative studies of the endonucleases from two related Xenopus laevis retrotransposons, Tx1L and Tx2L: target site specificity and evolutionary implications.

Science.gov (United States)

Christensen, S; Pont-Kingdon, G; Carroll, D

2000-01-01

In the genome of the South African frog, Xenopus laevis, there are two complex families of transposable elements, Tx1 and Tx2, that have identical overall structures, but distinct sequences. In each family there are approximately 1500 copies of an apparent DNA-based element (Tx1D and Tx2D). Roughly 10% of these elements in each family are interrupted by a non-LTR retrotransposon (Tx1L and Tx2L). Each retrotransposon is flanked by a 23-bp target duplication of a specific D element sequence. In earlier work, we showed that the endonuclease domain (Tx1L EN) located in the second open reading frame (ORF2) of Tx1L encodes a protein that makes a single-strand cut precisely at the expected site within its target sequence, supporting the idea that Tx1L is a site-specific retrotransposon. In this study, we express the endonuclease domain of Tx2L (Tx2L EN) and compare the target preferences of the two enzymes. Each endonuclease shows some preference for its cognate target, on the order of 5-fold over the non-cognate target. The observed discrimination is not sufficient, however, to explain the observation that no cross-occupancy is observed - that is, L elements of one family have never been found within D elements of the other family. Possible sources of additional specificity are discussed. We also compare two hypotheses regarding the genome duplication event that led to the contemporary pseudotetraploid character of Xenopus laevis in light of the Tx1L and Tx2L data.

Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand*

Science.gov (United States)

Teasley, Daniel C.; Parajuli, Shankar; Nguyen, Mai; Moore, Hayley R.; Alspach, Elise; Lock, Ying Jie; Honaker, Yuchi; Saharia, Abhishek; Piwnica-Worms, Helen; Stewart, Sheila A.

2015-01-01

The existence of redundant replication and repair systems that ensure genome stability underscores the importance of faithful DNA replication. Nowhere is this complexity more evident than in challenging DNA templates, including highly repetitive or transcribed sequences. Here, we demonstrate that flap endonuclease 1 (FEN1), a canonical lagging strand DNA replication protein, is required for normal, complete leading strand replication at telomeres. We find that the loss of FEN1 nuclease activity, but not DNA repair activities, results in leading strand-specific telomere fragility. Furthermore, we show that FEN1 depletion-induced telomere fragility is increased by RNA polymerase II inhibition and is rescued by ectopic RNase H1 expression. These data suggest that FEN1 limits leading strand-specific telomere fragility by processing RNA:DNA hybrid/flap intermediates that arise from co-directional collisions occurring between the replisome and RNA polymerase. Our data reveal the first molecular mechanism for leading strand-specific telomere fragility and the first known role for FEN1 in leading strand DNA replication. Because FEN1 mutations have been identified in human cancers, our findings raise the possibility that unresolved RNA:DNA hybrid structures contribute to the genomic instability associated with cancer. PMID:25922071

Time-Dependent-Asymmetric-Linear-Parsimonious Ancestral State Reconstruction.

Science.gov (United States)

Didier, Gilles

2017-10-01

The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony. This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated with the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.

Mechanochemistry assisted asymmetric organocatalysis: A sustainable approach

Directory of Open Access Journals (Sweden)

Pankaj Chauhan

2012-12-01

Full Text Available Ball-milling and pestle and mortar grinding have emerged as powerful methods for the development of environmentally benign chemical transformations. Recently, the use of these mechanochemical techniques in asymmetric organocatalysis has increased. This review highlights the progress in asymmetric organocatalytic reactions assisted by mechanochemical techniques.

Ideal 3D asymmetric concentrator

Energy Technology Data Exchange (ETDEWEB)

Garcia-Botella, Angel [Departamento Fisica Aplicada a los Recursos Naturales, Universidad Politecnica de Madrid, E.T.S.I. de Montes, Ciudad Universitaria s/n, 28040 Madrid (Spain); Fernandez-Balbuena, Antonio Alvarez; Vazquez, Daniel; Bernabeu, Eusebio [Departamento de Optica, Universidad Complutense de Madrid, Fac. CC. Fisicas, Ciudad Universitaria s/n, 28040 Madrid (Spain)

2009-01-15

Nonimaging optics is a field devoted to the design of optical components for applications such as solar concentration or illumination. In this field, many different techniques have been used for producing reflective and refractive optical devices, including reverse engineering techniques. In this paper we apply photometric field theory and elliptic ray bundles method to study 3D asymmetric - without rotational or translational symmetry - concentrators, which can be useful components for nontracking solar applications. We study the one-sheet hyperbolic concentrator and we demonstrate its behaviour as ideal 3D asymmetric concentrator. (author)

Rational design of coaxial mesoporous birnessite manganese dioxide/amorphous-carbon nanotubes arrays for advanced asymmetric supercapacitors

KAUST Repository

Zhu, Shijin; Zhang, Jie; Ma, Junjun; Zhang, Yuxin; Yao, Kexin

2015-01-01

Coaxial mesoporous MnO2/amorphous-carbon nanotubes have been synthesized via a facile and cost-effective strategy at room temperature. The coaxial double nanotubes of inner (outer) MnO2 and outer (inner) amorphous carbon can be obtained via fine tuning the preparative factors (e.g., deposition order and processing temperature). Furthermore, the electrochemical properties of the coaxial nanotubes were evaluated by cycle voltammetric (CV) and galvanostatic charge-discharge (GC) measurements. The as-prepared coaxial double nanotubes of outer MnO2 and inner amorphous carbon exhibit the optimized pseudocapacitance performance (362 F g-1) with good cycling stability, and ideal rate capability owning to the unique nanostructures. When assembled into two-electrode asymmetric supercapacitor, an energy density of 22.56 W h kg-1 at a power density of 224.9 W kg-1 is obtained. These findings provide a new and facile approach to fabricate high-performance electrode for supercapacitors.

Rational design of coaxial mesoporous birnessite manganese dioxide/amorphous-carbon nanotubes arrays for advanced asymmetric supercapacitors

KAUST Repository

Zhu, Shijin

2015-03-01

Coaxial mesoporous MnO2/amorphous-carbon nanotubes have been synthesized via a facile and cost-effective strategy at room temperature. The coaxial double nanotubes of inner (outer) MnO2 and outer (inner) amorphous carbon can be obtained via fine tuning the preparative factors (e.g., deposition order and processing temperature). Furthermore, the electrochemical properties of the coaxial nanotubes were evaluated by cycle voltammetric (CV) and galvanostatic charge-discharge (GC) measurements. The as-prepared coaxial double nanotubes of outer MnO2 and inner amorphous carbon exhibit the optimized pseudocapacitance performance (362 F g-1) with good cycling stability, and ideal rate capability owning to the unique nanostructures. When assembled into two-electrode asymmetric supercapacitor, an energy density of 22.56 W h kg-1 at a power density of 224.9 W kg-1 is obtained. These findings provide a new and facile approach to fabricate high-performance electrode for supercapacitors.

The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

Energy Technology Data Exchange (ETDEWEB)

Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.; Perry, J. Jefferson P.; Finger, L. David; Ng, Cliff; Tsai, Miaw-Sheue; Yannone, Steven M.; Tainer, John A.; Campisi, Judith; Cooper, Priscilla K.

2011-04-20

XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localize in nuclear foci. The co-localization was observed in mid- to late-S-phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain protein markers of both stalled replication forks and telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains, but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S-phase that is at least in part carried out coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.

Structural insights of the ssDNA binding site in the multifunctional endonuclease AtBFN2 from Arabidopsis thaliana.

Directory of Open Access Journals (Sweden)

Tsung-Fu Yu

Full Text Available The multi S1/P1 nuclease AtBFN2 (EC 3.1.30.1 encoded by the Arabidopsis thaliana At1g68290 gene is a glycoprotein that digests RNA, ssDNA, and dsDNA. AtBFN2 depends on three zinc ions for cleaving DNA and RNA at 3'-OH to yield 5'-nucleotides. In addition, AtBFN2's enzymatic activity is strongly glycan dependent. Plant Zn(2+-dependent endonucleases present a unique fold, and belong to the Phospholipase C (PLC/P1 nuclease superfamily. In this work, we present the first complete, ligand-free, AtBFN2 crystal structure, along with sulfate, phosphate and ssDNA co-crystal structures. With these, we were able to provide better insight into the glycan structure and possible enzymatic mechanism. In comparison with other nucleases, the AtBFN2/ligand-free and AtBFN2/PO4 models suggest a similar, previously proposed, catalytic mechanism. Our data also confirm that the phosphate and vanadate can inhibit the enzyme activity by occupying the active site. More importantly, the AtBFN2/A5T structure reveals a novel and conserved secondary binding site, which seems to be important for plant Zn(2+-dependent endonucleases. Based on these findings, we propose a rational ssDNA binding model, in which the ssDNA wraps itself around the protein and the attached surface glycan, in turn, reinforces the binding complex.

Asymmetric Supercapacitors Based on Reduced Graphene Oxide with Different Polyoxometalates as Positive and Negative Electrodes.

Science.gov (United States)

Dubal, Deepak P; Chodankar, Nilesh R; Vinu, Ajayan; Kim, Do-Heyoung; Gomez-Romero, Pedro

2017-07-10

Nanofabrication using a "bottom-up" approach of hybrid electrode materials into a well-defined architecture is essential for next-generation miniaturized energy storage devices. This paper describes the design and fabrication of reduced graphene oxide (rGO)/polyoxometalate (POM)-based hybrid electrode materials and their successful exploitation for asymmetric supercapacitors. First, redox active nanoclusters of POMs [phosphomolybdic acid (PMo 12 ) and phosphotungstic acid (PW 12 )] were uniformly decorated on the surface of rGO nanosheets to take full advantage of both charge-storing mechanisms (faradaic from POMs and electric double layer from rGO). The as-synthesized rGO-PMo 12 and rGO-PW 12 hybrid electrodes exhibited impressive electrochemical performances with specific capacitances of 299 (269 mF cm -2 ) and 370 F g -1 (369 mF cm -2 ) in 1 m H 2 SO 4 as electrolyte at 5 mA cm -2 . An asymmetric supercapacitor was then fabricated using rGO-PMo 12 as the positive and rGO-PW 12 as the negative electrode. This rGO-PMo 12 ∥rGO-PW 12 asymmetric cell could be successfully cycled in a wide voltage window up to 1.6 V and hence exhibited an excellent energy density of 39 Wh kg -1 (1.3 mWh cm -3 ) at a power density of 658 W kg -1 (23 mW cm -3 ). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Extreme triple asymmetric (ETAS) epitaxial designs for increased efficiency at high powers in 9xx-nm diode lasers

Science.gov (United States)

Kaul, T.; Erbert, G.; Maaßdorf, A.; Martin, D.; Crump, P.

2018-02-01

Broad area lasers that are tailored to be most efficient at the highest achievable optical output power are sought by industry to decrease operation costs and improve system performance. Devices using Extreme-Double-ASymmetric (EDAS) epitaxial designs are promising candidates for improved efficiency at high optical output powers due to low series resistance, low optical loss and low carrier leakage. However, EDAS designs leverage ultra-thin p-side waveguides, meaning that the optical mode is shifted into the n-side waveguide, resulting in a low optical confinement in the active region, low gain and hence high threshold current, limiting peak performance. We introduce here explicit design considerations that enable EDAS-based devices to be developed with increased optical confinement in the active layer without changing the p-side layer thicknesses. Specifically, this is realized by introducing a third asymmetric component in the vicinity of the quantum well. We call this approach Extreme-Triple-ASymmetric (ETAS) design. A series of ETAS-based vertical designs were fabricated into broad area lasers that deliver up to 63% power conversion efficiency at 14 W CW optical output power from a 100 μm stripe laser, which corresponds to the operation point of a kW optical output power in a laser bar. The design process, the impact of structural changes on power saturation mechanisms and finally devices with improved performance will be presented.

Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

DEFF Research Database (Denmark)

Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta

2014-01-01

The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease...... digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...... individuals using only 24 barcoded libraries....

Asymmetric hindwing foldings in rove beetles.

Science.gov (United States)

Saito, Kazuya; Yamamoto, Shuhei; Maruyama, Munetoshi; Okabe, Yoji

2014-11-18

Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use.

Enhancing Security of Double Random Phase Encoding Based on Random S-Box

Science.gov (United States)

Girija, R.; Singh, Hukum

2018-06-01

In this paper, we propose a novel asymmetric cryptosystem for double random phase encoding (DRPE) using random S-Box. While utilising S-Box separately is not reliable and DRPE does not support non-linearity, so, our system unites the effectiveness of S-Box with an asymmetric system of DRPE (through Fourier transform). The uniqueness of proposed cryptosystem lies on employing high sensitivity dynamic S-Box for our DRPE system. The randomness and scalability achieved due to applied technique is an additional feature of the proposed solution. The firmness of random S-Box is investigated in terms of performance parameters such as non-linearity, strict avalanche criterion, bit independence criterion, linear and differential approximation probabilities etc. S-Boxes convey nonlinearity to cryptosystems which is a significant parameter and very essential for DRPE. The strength of proposed cryptosystem has been analysed using various parameters such as MSE, PSNR, correlation coefficient analysis, noise analysis, SVD analysis, etc. Experimental results are conferred in detail to exhibit proposed cryptosystem is highly secure.

Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: Role of the LINE-encoded endonuclease

Directory of Open Access Journals (Sweden)

Gupta Abhishek K

2011-05-01

Full Text Available Abstract Background Entamoeba histolytica and Entamoeba dispar are closely related protistan parasites but while E. histolytica can be invasive, E. dispar is completely non pathogenic. Transposable elements constitute a significant portion of the genome in these species; there being three families of LINEs and SINEs. These elements can profoundly influence the expression of neighboring genes. Thus their genomic location can have important phenotypic consequences. A genome-wide comparison of the location of these elements in the E. histolytica and E. dispar genomes has not been carried out. It is also not known whether the retrotransposition machinery works similarly in both species. The present study was undertaken to address these issues. Results Here we extracted all genomic occurrences of full-length copies of EhSINE1 in the E. histolytica genome and matched them with the homologous regions in E. dispar, and vice versa, wherever it was possible to establish synteny. We found that only about 20% of syntenic sites were occupied by SINE1 in both species. We checked whether the different genomic location in the two species was due to differences in the activity of the LINE-encoded endonuclease which is required for nicking the target site. We found that the endonucleases of both species were essentially very similar, both in their kinetic properties and in their substrate sequence specificity. Hence the differential distribution of SINEs in these species is not likely to be influenced by the endonuclease. Further we found that the physical properties of the DNA sequences adjoining the insertion sites were similar in both species. Conclusions Our data shows that the basic retrotransposition machinery is conserved in these sibling species. SINEs may indeed have occupied all of the insertion sites in the genome of the common ancestor of E. histolytica and E. dispar but these may have been subsequently lost from some locations. Alternatively, SINE

Asymmetric Aldol Additions: A Guided-Inquiry Laboratory Activity on Catalysis

Science.gov (United States)

King, Jorge H. Torres; Wang, Hong; Yezierski, Ellen J.

2018-01-01

Despite the importance of asymmetric catalysis in both the pharmaceutical and commodity chemicals industries, asymmetric catalysis is under-represented in undergraduate chemistry laboratory curricula. A novel guided-inquiry experiment based on the asymmetric aldol addition was developed. Students conduct lab work to compare the effectiveness of…

Parallel coupling of symmetric and asymmetric exclusion processes

International Nuclear Information System (INIS)

Tsekouras, K; Kolomeisky, A B

2008-01-01

A system consisting of two parallel coupled channels where particles in one of them follow the rules of totally asymmetric exclusion processes (TASEP) and in another one move as in symmetric simple exclusion processes (SSEP) is investigated theoretically. Particles interact with each other via hard-core exclusion potential, and in the asymmetric channel they can only hop in one direction, while on the symmetric lattice particles jump in both directions with equal probabilities. Inter-channel transitions are also allowed at every site of both lattices. Stationary state properties of the system are solved exactly in the limit of strong couplings between the channels. It is shown that strong symmetric couplings between totally asymmetric and symmetric channels lead to an effective partially asymmetric simple exclusion process (PASEP) and properties of both channels become almost identical. However, strong asymmetric couplings between symmetric and asymmetric channels yield an effective TASEP with nonzero particle flux in the asymmetric channel and zero flux on the symmetric lattice. For intermediate strength of couplings between the lattices a vertical-cluster mean-field method is developed. This approximate approach treats exactly particle dynamics during the vertical transitions between the channels and it neglects the correlations along the channels. Our calculations show that in all cases there are three stationary phases defined by particle dynamics at entrances, at exits or in the bulk of the system, while phase boundaries depend on the strength and symmetry of couplings between the channels. Extensive Monte Carlo computer simulations strongly support our theoretical predictions. Theoretical calculations and computer simulations predict that inter-channel couplings have a strong effect on stationary properties. It is also argued that our results might be relevant for understanding multi-particle dynamics of motor proteins

Multipartite asymmetric quantum cloning

International Nuclear Information System (INIS)

Iblisdir, S.; Gisin, N.; Acin, A.; Cerf, N.J.; Filip, R.; Fiurasek, J.

2005-01-01

We investigate the optimal distribution of quantum information over multipartite systems in asymmetric settings. We introduce cloning transformations that take N identical replicas of a pure state in any dimension as input and yield a collection of clones with nonidentical fidelities. As an example, if the clones are partitioned into a set of M A clones with fidelity F A and another set of M B clones with fidelity F B , the trade-off between these fidelities is analyzed, and particular cases of optimal N→M A +M B cloning machines are exhibited. We also present an optimal 1→1+1+1 cloning machine, which is an example of a tripartite fully asymmetric cloner. Finally, it is shown how these cloning machines can be optically realized

Seasonally asymmetric enhancement of northern vegetation productivity

Science.gov (United States)

Park, T.; Myneni, R.

2017-12-01

Multiple evidences of widespread greening and increasing terrestrial carbon uptake have been documented. In particular, enhanced gross productivity of northern vegetation has been a critical role leading to observed carbon uptake trend. However, seasonal photosynthetic activity and its contribution to observed annual carbon uptake trend and interannual variability are not well understood. Here, we introduce a multiple-source of datasets including ground, atmospheric and satellite observations, and multiple process-based global vegetation models to understand how seasonal variation of land surface vegetation controls a large-scale carbon exchange. Our analysis clearly shows a seasonally asymmetric enhancement of northern vegetation productivity in growing season during last decades. Particularly, increasing gross productivity in late spring and early summer is obvious and dominant driver explaining observed trend and variability. We observe more asymmetric productivity enhancement in warmer region and this spatially varying asymmetricity in northern vegetation are likely explained by canopy development rate, thermal and light availability. These results imply that continued warming may facilitate amplifying asymmetric vegetation activity and cause these trends to become more pervasive, in turn warming induced regime shift in northern land.

Asymmetric Price Responses of Gasoline Stations. Evidence for Heterogeneity of Retailers

Energy Technology Data Exchange (ETDEWEB)

Faber, R.P. [Erasmus University Rotterdam, Rotterdam (Netherlands)

2009-11-15

This paper studies asymmetric price responses of individual firms, via daily retail prices of almost all gasoline stations in the Netherlands and suggested prices of the five largest oil companies over more than two years. I find that 38% of the stations respond asymmetrically to changes in the spot market price. Hence, asymmetric pricing is not a feature of the market as a whole, but of individual firms. For asymmetrically pricing stations, the asymmetry is substantial directly after a change but disappears after one or two days. I study station-specific characteristics and conclude that asymmetric pricing seems to be a phenomenon that is randomly distributed across stations. I also find that none of the five largest oil companies adjust their suggested prices asymmetrically.

Asymmetric Price Responses of Gasoline Stations. Evidence for Heterogeneity of Retailers

International Nuclear Information System (INIS)

Faber, R.P.

2009-11-01

This paper studies asymmetric price responses of individual firms, via daily retail prices of almost all gasoline stations in the Netherlands and suggested prices of the five largest oil companies over more than two years. I find that 38% of the stations respond asymmetrically to changes in the spot market price. Hence, asymmetric pricing is not a feature of the market as a whole, but of individual firms. For asymmetrically pricing stations, the asymmetry is substantial directly after a change but disappears after one or two days. I study station-specific characteristics and conclude that asymmetric pricing seems to be a phenomenon that is randomly distributed across stations. I also find that none of the five largest oil companies adjust their suggested prices asymmetrically.

Symmetry breaking states of Bose-Einstein condensates in 1D double square well and optical lattice well

International Nuclear Information System (INIS)

Yuan Qingxin; Ding Guohui

2005-01-01

We investigate the phenomena of symmetry breaking and phase transition in the ground state of Bose-Einstein condensates (BECs). For BECs trapped in a double square well potential, we present symmetric and asymmetric ground states by using standing-wave expansion method. For BECs trapped in an optical lattice well potential (created by a standing laser wave, and not just an extension of the double square well potential), we reveal a phase transition by using plane-wave expansion method. At the same time we also study the ground state properties with changing the depth of potential and atomic interactions (restrict ourselves to the attractive regime)

Observation of asymmetric electromagnetic field profiles in chiral metamaterials

Science.gov (United States)

Hisamoto, Nobuyuki; Ueda, Tetsuya; Sawada, Kei; Tomita, Satoshi

2018-02-01

We experimentally observe asymmetric electromagnetic field profiles along two-dimensional chiral metamaterials. The asymmetric field profiles depending on the chirality and the operation frequency have been reproduced well by the numerical simulation. Around a chiral meta-atom, distribution of a Poynting vector is found to be shifted asymmetrically. These results are explained in terms of an analogy with the side-jump mechanism in the electronic anomalous Hall systems.

Tuning of Preparational Factors Affecting the Morphological Structure and Gas Separation Property of Asymmetric Polysulfone Membranes

Science.gov (United States)

Yuenyao, C.; Ruangdit, S.; Chittrakarn, T.

2017-09-01

The aim of this work was to study the effect of preparational factors such as solvent type, evaporation time (ET) and non-solvent additive, on the morphological structure, physical and gas separation properties of the prepared membrane samples by tuning of these parameters. Flat sheet asymmetric polysulfone (PSF) membranes were prepared by the dry/wet phase inversion process combined with the double coagulation bath method. The alteration of the prepared membranes were analyzed through scientific techniques such as Scanning Electron Microscope (SEM) and Dynamic Mechanical Thermal Analysis (DMTA). Furthermore, gas separation performance of membrane samples was measured in term of gas permeation and ideal selectivity of CO2/CH4. Experimental results showed that the change of preparational factors affected to the gas permeation of asymmetric PSF membranes. For example, the selective layer thickness increased with increasing of ET. This lead to increase significantly of ideal selectivity of CO2/CH4. The CO2/CH4 ideal selectivity was also increased with increase of ethanol (non-solvent additive) concentration in casting solution. In summary, the tuning of preparational factors affected to morphological structure, physical and gas separation properties of PSF membranes.

A new convenient asymmetric approach to herbarumin Ⅲ

Institute of Scientific and Technical Information of China (English)

Xue Song Chen; Shi Jun Da; Li Hong Yang; Bo Yan Xu; Zhi Xiang Xie; Ying Li

2007-01-01

The asymmetric total synthesis of herbarumin Ⅲ 3, a naturally occurred phytotoxin, along with 8-epi-herbarumin Ⅲ 22, was succeeded in 12 steps from n-butyraldehyde based on Brown's asymmetric allylation, taking modified Julia olefination and Yamaguchi's macro-lactonization as key steps.

Fourier synthesis of asymmetrical optical potentials for atoms

International Nuclear Information System (INIS)

Ritt, G.

2007-01-01

In this work a dissipationless asymmetrical optical potential for cold atoms was produced. In a first step a new type of optical lattice was generated, whose spatial periodicity only corresponds to a quarter of the wavelength of the light used for the generation. This corresponds to the half of the periodicity of a conventional optical lattice, which is formed by the light of the same wavelength. The generation of this new type of optical lattice was reached by the use of two degenerated raman transitions. Virtual processes occur, in which four photons are involved. In conventional optical lattices however virtual two-photon processes occur. By spatially superimposing this optical lattice with a conventional optical lattice an asymmetrical optical potential could be formed. By diffraction of a Bose Einstein condensate of rubidium atoms at the transient activated asymmetrical potential the asymmetrical structure was proven. (orig.)

Engineered Asymmetric Composite Membranes with Rectifying Properties.

Science.gov (United States)

Wen, Liping; Xiao, Kai; Sainath, Annadanam V Sesha; Komura, Motonori; Kong, Xiang-Yu; Xie, Ganhua; Zhang, Zhen; Tian, Ye; Iyoda, Tomokazu; Jiang, Lei

2016-01-27

Asymmetric composite membranes with rectifying properties are developed by grafting pH-stimulus-responsive materials onto the top layer of the composite structure, which is prepared by two novel block copolymers using a phase-separation technique. This engineered asymmetric composite membrane shows potential applications in sensors, filtration, and nanofluidic devices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Micrococcus luteus correndonucleases. II. Mechanism of action of two endonucleases specific for DNA containing pyrimidine dimers

International Nuclear Information System (INIS)

Riazuddin, S.; Grossman, L.

1977-01-01

Py--Py correndonucleases I and II from Micrococcus luteus act exclusively on thymine-thymine, cytosine-cytosine, and thymine-cytosine cyclobutyl dimers in DNA, catalyzing incision 5' to the damage and generating 3'-hydroxyl and 5'-phosphoryl termini. Both enzymes initiate excision of pyrimidine dimers in vitro by correxonucleases and DNA polymerase I. The respective incised DNAs, however, differ in their ability to act as substrate for phage T4 polynucleotide ligase or bacterial alkaline phosphatase, suggesting that each endonuclease is specific for a conformationally unique site. The possibility that their respective action generates termini which represent different degrees of single strandedness is suggested by the unequal protection by Escherichia coli binding protein from the hydrolytic action of exonuclease VII

Pre-steady-state fluorescence analysis of damaged DNA transfer from human DNA glycosylases to AP endonuclease APE1.

Science.gov (United States)

Kuznetsova, Alexandra A; Kuznetsov, Nikita A; Ishchenko, Alexander A; Saparbaev, Murat K; Fedorova, Olga S

2014-10-01

DNA glycosylases remove the modified, damaged or mismatched bases from the DNA by hydrolyzing the N-glycosidic bonds. Some enzymes can further catalyze the incision of a resulting abasic (apurinic/apyrimidinic, AP) site through β- or β,δ-elimination mechanisms. In most cases, the incision reaction of the AP-site is catalyzed by special enzymes called AP-endonucleases. Here, we report the kinetic analysis of the mechanisms of modified DNA transfer from some DNA glycosylases to the AP endonuclease, APE1. The modified DNA contained the tetrahydrofurane residue (F), the analogue of the AP-site. DNA glycosylases AAG, OGG1, NEIL1, MBD4(cat) and UNG from different structural superfamilies were used. We found that all DNA glycosylases may utilise direct protein-protein interactions in the transient ternary complex for the transfer of the AP-containing DNA strand to APE1. We hypothesize a fast "flip-flop" exchange mechanism of damaged and undamaged DNA strands within this complex for monofunctional DNA glycosylases like MBD4(cat), AAG and UNG. Bifunctional DNA glycosylase NEIL1 creates tightly specific complex with DNA containing F-site thereby efficiently competing with APE1. Whereas APE1 fast displaces other bifunctional DNA glycosylase OGG1 on F-site thereby induces its shifts to undamaged DNA regions. Kinetic analysis of the transfer of DNA between human DNA glycosylases and APE1 allows us to elucidate the critical step in the base excision repair pathway. Copyright © 2014 Elsevier B.V. All rights reserved.

A large deformation viscoelastic model for double-network hydrogels

Science.gov (United States)

Mao, Yunwei; Lin, Shaoting; Zhao, Xuanhe; Anand, Lallit

2017-03-01

We present a large deformation viscoelasticity model for recently synthesized double network hydrogels which consist of a covalently-crosslinked polyacrylamide network with long chains, and an ionically-crosslinked alginate network with short chains. Such double-network gels are highly stretchable and at the same time tough, because when stretched the crosslinks in the ionically-crosslinked alginate network rupture which results in distributed internal microdamage which dissipates a substantial amount of energy, while the configurational entropy of the covalently-crosslinked polyacrylamide network allows the gel to return to its original configuration after deformation. In addition to the large hysteresis during loading and unloading, these double network hydrogels also exhibit a substantial rate-sensitive response during loading, but exhibit almost no rate-sensitivity during unloading. These features of large hysteresis and asymmetric rate-sensitivity are quite different from the response of conventional hydrogels. We limit our attention to modeling the complex viscoelastic response of such hydrogels under isothermal conditions. Our model is restricted in the sense that we have limited our attention to conditions under which one might neglect any diffusion of the water in the hydrogel - as might occur when the gel has a uniform initial value of the concentration of water, and the mobility of the water molecules in the gel is low relative to the time scale of the mechanical deformation. We also do not attempt to model the final fracture of such double-network hydrogels.

Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand.

Science.gov (United States)

Teasley, Daniel C; Parajuli, Shankar; Nguyen, Mai; Moore, Hayley R; Alspach, Elise; Lock, Ying Jie; Honaker, Yuchi; Saharia, Abhishek; Piwnica-Worms, Helen; Stewart, Sheila A

2015-06-12

The existence of redundant replication and repair systems that ensure genome stability underscores the importance of faithful DNA replication. Nowhere is this complexity more evident than in challenging DNA templates, including highly repetitive or transcribed sequences. Here, we demonstrate that flap endonuclease 1 (FEN1), a canonical lagging strand DNA replication protein, is required for normal, complete leading strand replication at telomeres. We find that the loss of FEN1 nuclease activity, but not DNA repair activities, results in leading strand-specific telomere fragility. Furthermore, we show that FEN1 depletion-induced telomere fragility is increased by RNA polymerase II inhibition and is rescued by ectopic RNase H1 expression. These data suggest that FEN1 limits leading strand-specific telomere fragility by processing RNA:DNA hybrid/flap intermediates that arise from co-directional collisions occurring between the replisome and RNA polymerase. Our data reveal the first molecular mechanism for leading strand-specific telomere fragility and the first known role for FEN1 in leading strand DNA replication. Because FEN1 mutations have been identified in human cancers, our findings raise the possibility that unresolved RNA:DNA hybrid structures contribute to the genomic instability associated with cancer. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

RECQ5 Helicase Cooperates with MUS81 Endonuclease in Processing Stalled Replication Forks at Common Fragile Sites during Mitosis

DEFF Research Database (Denmark)

Di Marco, Stefano; Hasanova, Zdenka; Kanagaraj, Radhakrishnan

2017-01-01

The MUS81-EME1 endonuclease cleaves late replication intermediates at common fragile sites (CFSs) during early mitosis to trigger DNA-repair synthesis that ensures faithful chromosome segregation. Here, we show that these DNA transactions are promoted by RECQ5 DNA helicase in a manner dependent...... on its Ser727 phosphorylation by CDK1. Upon replication stress, RECQ5 associates with CFSs in early mitosis through its physical interaction with MUS81 and promotes MUS81-dependent mitotic DNA synthesis. RECQ5 depletion or mutational inactivation of its ATP-binding site, RAD51-interacting domain...

Symmetry Breaking Ground States of Bose-Einstein Condensates in 1D Double Square Well and Optical Lattice Well

International Nuclear Information System (INIS)

Yuan Qingxin; Ding Guohui

2005-01-01

We investigate the phenomena of symmetry breaking and phase transition in the ground state of Bose-Einstein condensates (BECs) trapped in a double square well and in an optical lattice well, respectively. By using standing-wave expansion method, we present symmetric and asymmetric ground state solutions of nonlinear Schroedinger equation (NLSE) with a symmetric double square well potential for attractive nonlinearity. In particular, we study the ground state wave function's properties by changing the depth of potential and atomic interactions (here we restrict ourselves to the attractive regime). By using the Fourier grid Hamiltonian method, we also reveal a phase transition of BECs trapped in one-dimensional optical lattice potential.

Chemical display of pyrimidine bases flipped out by modification-dependent restriction endonucleases of MspJI and PvuRts1I families.

Directory of Open Access Journals (Sweden)

Evelina Zagorskaitė

Full Text Available The epigenetic DNA modifications 5-methylcytosine (5mC and 5-hydroxymethylcytosine (5hmC in eukaryotes are recognized either in the context of double-stranded DNA (e.g., by the methyl-CpG binding domain of MeCP2, or in the flipped-out state (e.g., by the SRA domain of UHRF1. The SRA-like domains and the base-flipping mechanism for 5(hmC recognition are also shared by the recently discovered prokaryotic modification-dependent endonucleases of the MspJI and PvuRts1I families. Since the mechanism of modified cytosine recognition by many potential eukaryotic and prokaryotic 5(hmC "readers" is still unknown, a fast solution based method for the detection of extrahelical 5(hmC would be very useful. In the present study we tested base-flipping by MspJI- and PvuRts1I-like restriction enzymes using several solution-based methods, including fluorescence measurements of the cytosine analog pyrrolocytosine and chemical modification of extrahelical pyrimidines with chloroacetaldehyde and KMnO4. We find that only KMnO4 proved an efficient probe for the positive display of flipped out pyrimidines, albeit the method required either non-physiological pH (4.3 or a substitution of the target cytosine with thymine. Our results imply that DNA recognition mechanism of 5(hmC binding proteins should be tested using a combination of all available methods, as the lack of a positive signal in some assays does not exclude the base flipping mechanism.

Decrease in back strength in asymmetric trunk postures

NARCIS (Netherlands)

Vink, P.; Daanen, H. A M; Meijst, W. J.; Ligteringen, J.

1992-01-01

The extension force against resistance was recorded in 23 postures for 12 subjects to find explanations for the decrease in back strength in asymmetric postures. A reduction in muscle force in asymmetric postures was found up to 40%, but was strongly dependent on the plane in which asymmetry

Subglottic cysts and asymmetrical subglottic narrowing on neck radiograph

International Nuclear Information System (INIS)

Holinger, L.D.; Torium, D.M.; Anandappa, E.C.

1988-01-01

The congenital subglottic hemangioma typically appears as an asymmetric subglottic narrowing or mass on frontal neck radiograph. Therefore, soft tissue neck radiography has been advocated as a definitive non-operative approach for diagnosing these lesions. However, we have noted similar asymmetric subglottic narrowing in patients with acquired subglottic cysts. These retention cysts occur following long-term intubation in the neonate. The mechanism probably involves subglottic fibrosis which obstructs glands with subsequent cyst formation. Acquired subglottic cysts typically appear as an asymmetric narrowing on frontal or lateral soft tissue neck radiographs. These lesions may produce airway compromise but are effectively treated by forceps or laser removal. Acquired subglottic cysts must be included in the differential diagnosis of asymmetric subglottic narrowing. The definitive diagnosis is made by direct laryngoscopy, not soft tissue neck radiograph. (orig.)

Lower Bounds in the Asymmetric External Memory Model

DEFF Research Database (Denmark)

Jacob, Riko; Sitchinava, Nodari

2017-01-01

Motivated by the asymmetric read and write costs of emerging non-volatile memory technologies, we study lower bounds for the problems of sorting, permuting and multiplying a sparse matrix by a dense vector in the asymmetric external memory model (AEM). Given an AEM with internal (symmetric) memory...... of size M, transfers between symmetric and asymmetric memory in blocks of size B and the ratio ω between write and read costs, we show Ω(min (N, ωN/B logω M/B N/B) lower bound for the cost of permuting N input elements. This lower bound also applies to the problem of sorting N elements. This proves...

Primary processing of CRISPR RNA by the endonuclease Cas6 in Staphylococcus epidermidis.

Science.gov (United States)

Wakefield, Noelle; Rajan, Rakhi; Sontheimer, Erik J

2015-10-07

In many bacteria and archaea, an adaptive immune system (CRISPR-Cas) provides immunity against foreign genetic elements. This system uses CRISPR RNAs (crRNAs) derived from the CRISPR array, along with CRISPR-associated (Cas) proteins, to target foreign nucleic acids. In most CRISPR systems, endonucleolytic processing of crRNA precursors (pre-crRNAs) is essential for the pathway. Here we study the Cas6 endonuclease responsible for crRNA processing in the Type III-A CRISPR-Cas system from Staphylococcus epidermidis RP62a, a model for Type III-A CRISPR-Cas systems, and define substrate requirements for SeCas6 activity. We find that SeCas6 is necessary and sufficient for full-length crRNA biogenesis in vitro, and that it relies on both sequence and stem-loop structure in the 3' half of the CRISPR repeat for recognition and processing. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Double valley Dirac fermions for 3D and 2D Hg1-x Cd x Te with strong asymmetry

Science.gov (United States)

Marchewka, M.

2017-04-01

In this paper the possibility to bring about the double-valley Dirac fermions in some quantum structures is predicted. These quantum structures are: strained 3D Hg1-x Cd x Te topological insulator (TI) with strong interface inversion asymmetry and the asymmetric Hg1-x Cd x Te double quantum wells (DQW). The numerical analysis of the dispersion relation for 3D TI Hg1-x Cd x Te for the proper Cd (x)-content of the Hg1-x Cd x Te compound clearly shows that the inversion symmetry breaking together with the unaxial tensile strain causes the splitting of each of the Dirac nodes (two belonging to two interfaces) into two in the proximity of the Γ-point. Similar effects can be obtained for asymmetric Hg1-x Cd x Te DQW with the proper content of Cd and proper width of the quantum wells. The aim of this work is to explore the inversion symmetry breaking in 3D TI and 2D DQW mixed HgCdTe systems. It is shown that this symmetry breaking leads to the dependence of carriers energy on quasi-momentum similar to that of Weyl fermions.

Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease

Directory of Open Access Journals (Sweden)

Francesco Gentile

2018-04-01

Full Text Available The DNA excision repair protein ERCC-1-DNA repair endonuclease XPF (ERCC1-XPF is a heterodimeric endonuclease essential for the nucleotide excision repair (NER DNA repair pathway. Although its activity is required to maintain genome integrity in healthy cells, ERCC1-XPF can counteract the effect of DNA-damaging therapies such as platinum-based chemotherapy in cancer cells. Therefore, a promising approach to enhance the effect of these therapies is to combine their use with small molecules, which can inhibit the repair mechanisms in cancer cells. Currently, there are no structures available for the catalytic site of the human ERCC1-XPF, which performs the metal-mediated cleavage of a DNA damaged strand at 5′. We adopted a homology modeling strategy to build a structural model of the human XPF nuclease domain which contained the active site and to extract dominant conformations of the domain using molecular dynamics simulations followed by clustering of the trajectory. We investigated the binding modes of known small molecule inhibitors targeting the active site to build a pharmacophore model. We then performed a virtual screening of the ZINC Is Not Commercial 15 (ZINC15 database to identify new ERCC1-XPF endonuclease inhibitors. Our work provides structural insights regarding the binding mode of small molecules targeting the ERCC1-XPF active site that can be used to rationally optimize such compounds. We also propose a set of new potential DNA repair inhibitors to be considered for combination cancer therapy strategies.

Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats.

Science.gov (United States)

Gabsalilow, Lilia; Schierling, Benno; Friedhoff, Peter; Pingoud, Alfred; Wende, Wolfgang

2013-04-01

Targeted genome engineering requires nucleases that introduce a highly specific double-strand break in the genome that is either processed by homology-directed repair in the presence of a homologous repair template or by non-homologous end-joining (NHEJ) that usually results in insertions or deletions. The error-prone NHEJ can be efficiently suppressed by 'nickases' that produce a single-strand break rather than a double-strand break. Highly specific nickases have been produced by engineering of homing endonucleases and more recently by modifying zinc finger nucleases (ZFNs) composed of a zinc finger array and the catalytic domain of the restriction endonuclease FokI. These ZF-nickases work as heterodimers in which one subunit has a catalytically inactive FokI domain. We present two different approaches to engineer highly specific nickases; both rely on the sequence-specific nicking activity of the DNA mismatch repair endonuclease MutH which we fused to a DNA-binding module, either a catalytically inactive variant of the homing endonuclease I-SceI or the DNA-binding domain of the TALE protein AvrBs4. The fusion proteins nick strand specifically a bipartite recognition sequence consisting of the MutH and the I-SceI or TALE recognition sequences, respectively, with a more than 1000-fold preference over a stand-alone MutH site. TALE-MutH is a programmable nickase.

Ultrathin-skinned asymmetric membranes by immiscible solvents treatment

Science.gov (United States)

Friesen, Dwayne T.; Babcock, Walter C.

1989-01-01

Improved semipermeable asymmetric fluid separation membranes useful in gas, vapor and liquid separations are disclosed. The membranes are prepared by substantially filling the pores of asymmetric cellulosic semipermeable membranes having a finely porous layer on one side thereof with a water immiscible organic liquid, followed by contacting the finely porous layer with water.

Mycobacterial nonhomologous end joining mediates mutagenic repair of chromosomal double-strand DNA breaks.

Science.gov (United States)

Stephanou, Nicolas C; Gao, Feng; Bongiorno, Paola; Ehrt, Sabine; Schnappinger, Dirk; Shuman, Stewart; Glickman, Michael S

2007-07-01

Bacterial nonhomologous end joining (NHEJ) is a recently described DNA repair pathway best characterized in mycobacteria. Bacterial NHEJ proteins LigD and Ku have been analyzed biochemically, and their roles in linear plasmid repair in vivo have been verified genetically; yet the contributions of NHEJ to repair of chromosomal DNA damage are unknown. Here we use an extensive set of NHEJ- and homologous recombination (HR)-deficient Mycobacterium smegmatis strains to probe the importance of HR and NHEJ in repairing diverse types of chromosomal DNA damage. An M. smegmatis Delta recA Delta ku double mutant has no apparent growth defect in vitro. Loss of the NHEJ components Ku and LigD had no effect on sensitivity to UV radiation, methyl methanesulfonate, or quinolone antibiotics. NHEJ deficiency had no effect on sensitivity to ionizing radiation in logarithmic- or early-stationary-phase cells but was required for ionizing radiation resistance in late stationary phase in 7H9 but not LB medium. In addition, NHEJ components were required for repair of I-SceI mediated chromosomal double-strand breaks (DSBs), and in the absence of HR, the NHEJ pathway rapidly mutates the chromosomal break site. The molecular outcomes of NHEJ-mediated chromosomal DSB repair involve predominantly single-nucleotide insertions at the break site, similar to previous findings using plasmid substrates. These findings demonstrate that prokaryotic NHEJ is specifically required for DSB repair in late stationary phase and can mediate mutagenic repair of homing endonuclease-generated chromosomal DSBs.

Asymmetric conditional volatility in international stock markets

Science.gov (United States)

Ferreira, Nuno B.; Menezes, Rui; Mendes, Diana A.

2007-08-01

Recent studies show that a negative shock in stock prices will generate more volatility than a positive shock of similar magnitude. The aim of this paper is to appraise the hypothesis under which the conditional mean and the conditional variance of stock returns are asymmetric functions of past information. We compare the results for the Portuguese Stock Market Index PSI 20 with six other Stock Market Indices, namely the SP 500, FTSE 100, DAX 30, CAC 40, ASE 20, and IBEX 35. In order to assess asymmetric volatility we use autoregressive conditional heteroskedasticity specifications known as TARCH and EGARCH. We also test for asymmetry after controlling for the effect of macroeconomic factors on stock market returns using TAR and M-TAR specifications within a VAR framework. Our results show that the conditional variance is an asymmetric function of past innovations raising proportionately more during market declines, a phenomenon known as the leverage effect. However, when we control for the effect of changes in macroeconomic variables, we find no significant evidence of asymmetric behaviour of the stock market returns. There are some signs that the Portuguese Stock Market tends to show somewhat less market efficiency than other markets since the effect of the shocks appear to take a longer time to dissipate.

Solutions for confluent and double-confluent Heun equations and some applications

Energy Technology Data Exchange (ETDEWEB)

El-Jaick, Lea Jaccoud; Figueiredo, Bartolomeu D.B. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)

2008-07-01

This paper examines some solutions for confluent and double-confluent Heun equations and their applications to the Schroedinger equation with quasi-exactly solvable potentials. In the first place, we review two Leaver's solutions in series of regular and irregular confluent hypergeometric functions for the confluent equation [E. W. Leaver, J. Math. Phys. 27, 1238 (1986)] and introduce an additional expansion in series of irregular confluent hypergeometric functions. Then, we find the conditions under which one of these solutions can be written as a linear combination of the others. In the second place, by means of limiting procedures we generate solutions for the double-confluent equation as well as for special limits of both the confluent and double-confluent equations. In the third place, solutions of the Heun equations are used to solve the one-dimensional Schroedinger equation for quasi-exactly solvable potentials. We consider a symmetric and an asymmetric double-Morse potentials which appear in the theory of quantum spin systems [O. B. Zaslavskii and V. V. Ulyanov, Sov. Phys. JETP 60, 991 (1984)], a bottomless volcano-type potential which gives degenerate eigenstates [S. Kar and R. R. Parwani, Europhys. Lett., 80, 30004 (2007)], and a potential which leads to quasi normal modes, that is, to solutions presenting complex energies [H. T. Cho and C. L. Ho, J. Phys. A: Math. Theor. 40, 1325 (2007)]. (author)

Solutions for confluent and double-confluent Heun equations and some applications

International Nuclear Information System (INIS)

El-Jaick, Lea Jaccoud; Figueiredo, Bartolomeu D.B.

2008-01-01

This paper examines some solutions for confluent and double-confluent Heun equations and their applications to the Schroedinger equation with quasi-exactly solvable potentials. In the first place, we review two Leaver's solutions in series of regular and irregular confluent hypergeometric functions for the confluent equation [E. W. Leaver, J. Math. Phys. 27, 1238 (1986)] and introduce an additional expansion in series of irregular confluent hypergeometric functions. Then, we find the conditions under which one of these solutions can be written as a linear combination of the others. In the second place, by means of limiting procedures we generate solutions for the double-confluent equation as well as for special limits of both the confluent and double-confluent equations. In the third place, solutions of the Heun equations are used to solve the one-dimensional Schroedinger equation for quasi-exactly solvable potentials. We consider a symmetric and an asymmetric double-Morse potentials which appear in the theory of quantum spin systems [O. B. Zaslavskii and V. V. Ulyanov, Sov. Phys. JETP 60, 991 (1984)], a bottomless volcano-type potential which gives degenerate eigenstates [S. Kar and R. R. Parwani, Europhys. Lett., 80, 30004 (2007)], and a potential which leads to quasi normal modes, that is, to solutions presenting complex energies [H. T. Cho and C. L. Ho, J. Phys. A: Math. Theor. 40, 1325 (2007)]. (author)

Salt supply to and significance of asymmetric salt diapirs

DEFF Research Database (Denmark)

Koyi, H.; Burliga, S.; Chemia, Zurab

2012-01-01

Salt diapirs can be asymmetric both internally and externally reflecting their evolution history. As such, this asymmetry bear a significant amount of information about the differential loading (± lateral forces) and in turn the salt supply that have shaped the diapir. In two dimensions......, In this study we compare results of analogue and numerical models of diapirs with two natural salt diapris (Klodawa and Gorleben diapirs) to explain their salt supply and asymmetric evolution. In a NW-SE section, the Gorleben salt diapir possesses an asymmetric external geometry represented by a large...... southeastern overhang due to salt extrusion during Middle Cretaceous followed by its burial in Tertiary. This external asymmetry is also reflected in the internal configuration of the diapir which shows different rates of salt flow on the two halves of the structure. The asymmetric external and internal...

Two-channel totally asymmetric simple exclusion processes

International Nuclear Information System (INIS)

Pronina, Ekaterina; Kolomeisky, Anatoly B

2004-01-01

Totally asymmetric simple exclusion processes, consisting of two coupled parallel lattice chains with particles interacting with hard-core exclusion and moving along the channels and between them, are considered. In the limit of strong coupling between the channels, the particle currents, density profiles and a phase diagram are calculated exactly by mapping the system into an effective one-channel totally asymmetric exclusion model. For intermediate couplings, a simple approximate theory, that describes the particle dynamics in vertical clusters of two corresponding parallel sites exactly and neglects the correlations between different vertical clusters, is developed. It is found that, similarly to the case of one-channel totally asymmetric simple exclusion processes, there are three stationary state phases, although the phase boundaries and stationary properties strongly depend on inter-channel coupling. Extensive computer Monte Carlo simulations fully support the theoretical predictions

Activation of apurinic/apyrimidinic endonuclease in human cells by reactive oxygen species and its correlation with their adaptive response to genotoxicity of free radicals

Science.gov (United States)

Ramana, Chilakamarti V.; Boldogh, Istvan; Izumi, Tadahide; Mitra, Sankar

1998-01-01

Apurinic/apyrimidinic (AP) endonuclease (APE; EC 4.2.99.18) plays a central role in repair of DNA damage due to reactive oxygen species (ROS) because its DNA 3′-phosphoesterase activity removes 3′ blocking groups in DNA that are generated by DNA glycosylase/AP-lyases during removal of oxidized bases and by direct ROS reaction with DNA. The major human APE (APE-1) gene is activated selectively by sublethal levels of a variety of ROS and ROS generators, including ionizing radiation, but not by other genotoxicants—e.g., UV light and alkylating agents. Increased expression of APE mRNA and protein was observed both in the HeLa S3 tumor line and in WI 38 primary fibroblasts, and it was accompanied by translocation of the endonuclease to the nucleus. ROS-treated cells showed a significant increase in resistance to the cytotoxicity of such ROS generators as H2O2 and bleomycin, but not to UV light. This “adaptive response” appears to result from enhanced repair of cytotoxic DNA lesions due to an increased activity of APE-1, which may be limiting in the base excision repair process for ROS-induced toxic lesions. PMID:9560228

Appropriate quantization of asymmetric games with continuous strategies

International Nuclear Information System (INIS)

Qin Gan; Chen Xi; Sun Min; Zhou Xianyi; Du Jiangfeng

2005-01-01

We establish a new quantization scheme to study the asymmetric Bertrand duopoly with differentiated products. This scheme is more efficient than the previous symmetric one because it can exactly make the optimal cooperative payoffs at quantum Nash equilibrium. It is also a necessary condition for general asymmetric games with continuous strategies to reach such payoffs

[Endonuclease modified comet assay for oxidative DNA damage induced by detection of genetic toxicants].

Science.gov (United States)

Zhao, Jian; Li, Hongli; Zhai, Qingfeng; Qiu, Yugang; Niu, Yong; Dai, Yufei; Zheng, Yuxin; Duan, Huawei

2014-03-01

The aim of this study was to investigate the use of the lesion-specific endonucleases-modified comet assay for analysis of DNA oxidation in cell lines. DNA breaks and oxidative damage were evaluated by normal alkaline and formamidopyrimidine-DNA-glycosylase (FPG) modified comet assays. Cytotoxicity were assessed by MTT method. The human bronchial epithelial cell (16HBE) were treated with benzo (a) pyrene (B(a)P), methyl methanesulfonate (MMS), colchicine (COL) and vincristine (VCR) respectively, and the dose is 20 µmol/L, 25 mg/ml, 5 mg/L and 0.5 mg/L for 24 h, respectively. Oxidative damage was also detected by levels of reactive oxygen species in treated cells. Four genotoxicants give higher cytotoxicity and no significant changes on parameters of comet assay treated by enzyme buffer. Cell survival rate were (59.69 ± 2.60) %, (54.33 ± 2.81) %, (53.11 ± 4.00) %, (51.43 ± 3.92) % in four groups, respectively. There was the direct DNA damage induced by test genotoxicants presented by tail length, Olive tail moment (TM) and tail DNA (%) in the comet assay. The presence of FPG in the assays increased DNA migration in treated groups when compared to those without it, and the difference was statistically significant which indicated that the clastogen and aneugen could induce oxidative damage in DNA strand. In the three parameters, the Olive TM was changed most obviously after genotoxicants treatment. In the contrast group, the Olive TM of B(a) P,MMS, COL,VCR in the contrast groups were 22.99 ± 17.33, 31.65 ± 18.86, 19.86 ± 9.56 and 17.02 ± 9.39, respectively, after dealing with the FPG, the Olive TM were 34.50 ± 17.29, 43.80 ± 10.06, 33.10 ± 12.38, 28.60 ± 10.53, increased by 58.94%, 38.48%, 66.86% and 68.21%, respectively (t value was 3.91, 3.89, 6.66 and 3.87, respectively, and all P comet assay appears more specific for detecting oxidative DNA damage induced by genotoxicants exposure, and the application of comet assay will be expanded. The endonuclease

Asymmetric forecasting and commitment policy in a robust control problem

OpenAIRE

Taro Ikeda

2013-01-01

This paper provides a piece of results regarding asymmetric forecasting and commitment monetary policy with a robust control algorithm. Previous studies provide no clarification of the connection between asymmetric preference and robust commitment policy. Three results emerge from general equilibrium modeling with asymmetric preference: (i) the condition for system stability implies an average inflation bias with respect to asymmetry (ii) the effect of asymmetry can be mitigated if policy mak...

Epigastric heteropagus associated with an omphalocele and double outlet right ventricle

Directory of Open Access Journals (Sweden)

Tatsuma Sakaguchi

2015-10-01

Full Text Available Incomplete or asymmetrical conjoined twins are extremely rare congenital anomalies. We report a case of epigastric heteropagus associated with an omphalocele and double outlet right ventricle. The cystic legion of the epigastrium was detected in our patient by an ultrasound scan at 28 weeks' gestation. He was born at 37 weeks' gestation by scheduled caesarean section. A parasite with an incomplete head and lower limb was attached to the epigastrium of the autosite. Surgical separation of the parasite and silo placement for an omphalocele was successfully performed on the 4th day of life. He underwent secondary surgical closure of the omphalocele on the 10th day. For treatment of the cardiac anomaly, he underwent an operation of Blalock–Taussig shunt because of pulmonary artery stenosis at the age of 3 months and correction of double outlet right ventricle at the age of 10 months. At the 20-month follow-up, he was alive and showed a normal growth pattern.

Impact of Secondary Interactions in Asymmetric Catalysis

OpenAIRE

Frölander, Anders

2007-01-01

This thesis deals with secondary interactions in asymmetric catalysis and their impact on the outcome of catalytic reactions. The first part revolves around the metal-catalyzed asymmetric allylic alkylation reaction and how interactions within the catalyst affect the stereochemistry. An OH–Pd hydrogen bond in Pd(0)–π-olefin complexes of hydroxy-containing oxazoline ligands was identified by density functional theory computations and helped to rationalize the contrasting results obtained emplo...

How Is Nature Asymmetric?

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 6. How Is Nature Asymmetric? - Discrete Symmetries in Particle Physics and their Violation ... Indian Institute of Technology, Chennai. Aligarh Muslim University. University of Rajasthan, Jaipur. Indian Institute of Science, Bangalore 560012, India.

Exploring asymmetric catalytic transformations

NARCIS (Netherlands)

Guduguntla, Sureshbabu

2017-01-01

In Chapter 2, we report a highly enantioselective synthesis of β-alkyl-substituted alcohols through a one-pot Cu- catalyzed asymmetric allylic alkylation with organolithium reagents followed by reductive ozonolysis. The synthesis of γ-alkyl-substituted alcohols was also achieved through Cu-catalyzed

Simulation of Phenix EOL Asymmetric Test

Energy Technology Data Exchange (ETDEWEB)

Ha, Kwi Seok; Lee, Kwi Lim; Choi, Chi Woong; Kang, Seok Hun; Chang, Won Pyo; Jeong, Hae Yong [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2012-05-15

The asymmetric test of End-Of-Life (EOL) tests on the Phenix plant was used for the evaluation of the MARS-LMR in the Generation IV frame as a part of the code validation. The purpose of the test is to evaluate the ability of the system code to describe asymmetric situations and to identify important phenomena during asymmetrical transient such as a three dimensional effect, buoyancy influence, and thermal stratification in the hot and cold pools. 3-dimensional sodium coolant mixing in the pools has different characteristics from the one dimensional full instantaneous mixing. The velocities and temperatures at the core outlet level differ at each sub-assembly and the temperature in the center of the hot pool may be high because the driver fuels are located at the center region. The temperatures in the hot pool are not the same in the radial and axial locations due to the buoyancy effect. The temperatures in the cold pool also differ along with the elevations and azimuthal directions due to the outlet location of IHX and the thermal stratification

Flatfish: an asymmetric perspective on metamorphosis.

Science.gov (United States)

Schreiber, Alexander M

2013-01-01

The most asymmetrically shaped and behaviorally lateralized of all the vertebrates, the flatfishes are an endless source of fascination to all fortunate enough to study them. Although all vertebrates undergo left-right asymmetric internal organ placement during embryogenesis, flatfish are unusual in that they experience an additional period of postembryonic asymmetric remodeling during metamorphosis, and thus deviate from a bilaterally symmetrical body plan more than other vertebrates. As with amphibian metamorphosis, all the developmental programs of flatfish metamorphosis are ultimately under the control of thyroid hormone. At least one gene pathway involved in embryonic organ lateralization (nodal-lefty-pitx2) is re-expressed in the larval stage during flatfish metamorphosis. Aspects of modern flatfish ontogeny, such as the gradual translocation of one eye to the opposite side of the head and the appearance of key neurocranial elements during metamorphosis, seem to elegantly recapitulate flatfish phylogeny. This chapter highlights the current state of knowledge of the developmental biology of flatfish metamorphosis with emphases on the genetic, morphological, behavioral, and evolutionary origins of flatfish asymmetry. Copyright © 2013 Elsevier Inc. All rights reserved.

Standards vs. labels with imperfect competition and asymmetric information

DEFF Research Database (Denmark)

Baltzer, Kenneth Thomas

2012-01-01

I demonstrate that providing information about product quality is not necessarily the best way to address asymmetric information problems when markets are imperfectly competitive. In a vertical differentiation model I show that a Minimum Quality Standard, which retains asymmetric information...

Standards vs. labels with imperfect competition and asymmetric information

DEFF Research Database (Denmark)

Baltzer, Kenneth Thomas

I demonstrate that providing information about product quality is not necessarily the best way to address asymmetric information problems when markets are imperfectly competitive. In a vertical dierentiation model I show that a Minimum Quality Standard, which retains asymmetric information...

Indirect double photoionization of water

Science.gov (United States)

Resccigno, T. N.; Sann, H.; Orel, A. E.; Dörner, R.

2011-05-01

The vertical double ionization thresholds of small molecules generally lie above the dissociation limits corresponding to formation of two singly charged fragments. This gives the possibility of populating singly charged molecular ions by photoionization in the Franck-Condon region at energies below the lowest dication state, but above the dissociation limit into two singly charged fragment ions. This process can produce a superexcited neutral fragment that autoionizes at large internuclear separation. We study this process in water, where absorption of a photon produces an inner-shell excited state of H2O+ that fragments to H++OH*. The angular distribution of secondary electrons produced by OH* when it autoionizes produces a characteristic asymmetric pattern that reveals the distance, and therefore the time, at which the decay takes place. LBNL, Berkeley, CA, J. W. Goethe Universität, Frankfurt, Germany. Work performed under auspices of US DOE and supported by OBES, Div. of Chemical Sciences.

Suppressed power saturation due to optimized optical confinement in 9xx nm high-power diode lasers that use extreme double asymmetric vertical designs

Science.gov (United States)

Kaul, T.; Erbert, G.; Maaßdorf, A.; Knigge, S.; Crump, P.

2018-03-01

Broad area lasers with novel extreme double asymmetric structure (EDAS) vertical designs featuring increased optical confinement in the quantum well, Γ, are shown to have improved temperature stability without compromising series resistance, internal efficiency or losses. Specifically, we present here vertical design considerations for the improved continuous wave (CW) performance of devices operating at 940 nm, based on systematically increasing Γ from 0.26% to 1.1%, and discuss the impact on power saturation mechanisms. The results indicate that key power saturation mechanisms at high temperatures originate in high threshold carrier densities, which arise in the quantum well at low Γ. The characteristic temperatures, T 0 and T 1, are determined under short pulse conditions and are used to clarify the thermal contribution to power limiting mechanisms. Although increased Γ reduces thermal power saturation, it is accompanied by increased optical absorption losses in the active region, which has a significant impact on the differential external quantum efficiency, {η }{{diff}}. To quantify the impact of internal optical losses contributed by the quantum well, a resonator length-dependent simulation of {η }{{diff}} is performed and compared to the experiment, which also allows the estimation of experimental values for the light absorption cross sections of electrons and holes inside the quantum well. Overall, the analysis enables vertical designs to be developed, for devices with maximized power conversion efficiency at high CW optical power and high temperatures, in a trade-off between absorption in the well and power saturation. The best balance to date is achieved in devices using EDAS designs with {{Γ }}=0.54 % , which deliver efficiencies of 50% at 14 W optical output power at an elevated junction temperature of 105 °C.

Asymmetrical Polymer Vesicles for Drug delivery and Other Applications

Directory of Open Access Journals (Sweden)

Yi Zhao

2017-06-01

Full Text Available Scientists have been attracted by polymersomes as versatile drug delivery systems since the last two decades. Polymersomes have the potential to be versatile drug delivery systems because of their tunable membrane formulations, stabilities in vivo, various physicochemical properties, controlled release mechanisms, targeting abilities, and capacities to encapsulate a wide range of drugs and other molecules. Asymmetrical polymersomes are nano- to micro-sized polymeric capsules with asymmetrical membranes, which means, they have different outer and inner coronas so that they can exhibit better endocytosis rate and endosomal escape ability than other polymeric systems with symmetrical membranes. Hence, asymmetrical polymersomes are highly promising as self-assembled nano-delivery systems in the future for in vivo therapeutics delivery and diagnostic imaging applications. In this review, we prepared a summary about recent research progresses of asymmetrical polymersomes in the following aspects: synthesis, preparation, applications in drug delivery and others.

Twist limits for late twisting double somersaults on trampoline.

Science.gov (United States)

Yeadon, M R; Hiley, M J

2017-06-14

An angle-driven computer simulation model of aerial movement was used to determine the maximum amount of twist that could be produced in the second somersault of a double somersault on trampoline using asymmetrical movements of the arms and hips. Lower bounds were placed on the durations of arm and hip angle changes based on performances of a world trampoline champion whose inertia parameters were used in the simulations. The limiting movements were identified as the largest possible odd number of half twists for forward somersaulting takeoffs and even number of half twists for backward takeoffs. Simulations of these two limiting movements were found using simulated annealing optimisation to produce the required amounts of somersault, tilt and twist at landing after a flight time of 2.0s. Additional optimisations were then run to seek solutions with the arms less adducted during the twisting phase. It was found that 3½ twists could be produced in the second somersault of a forward piked double somersault with arms abducted 8° from full adduction during the twisting phase and that three twists could be produced in the second somersault of a backward straight double somersault with arms fully adducted to the body. These two movements are at the limits of performance for elite trampolinists. Copyright © 2017 Elsevier Ltd. All rights reserved.

Catalytic asymmetric dihydroxylation of olefins with reusable OsO(4)(2-) on ion-exchangers: the scope and reactivity using various cooxidants.

Science.gov (United States)

Choudary, Boyapati M; Chowdari, Naidu S; Jyothi, Karangula; Kantam, Mannepalli L

2002-05-15

Exchanger-OsO(4) catalysts are prepared by an ion-exchange technique using layered double hydroxides and quaternary ammonium salts covalently bound to resin and silica as ion-exchangers. The ion-exchangers with different characteristics and opposite ion selectivities are specially chosen to produce the best heterogeneous catalyst that can operate using the various cooxidants in the asymmetric dihydroxylation reaction. LDH-OsO(4) catalysts composed of different compositions are evaluated for the asymmetric dihydroxylation of trans-stilbene. Resin-OsO(4) and SiO(2)-OsO(4) designed to overcome the problems associated with LDH-OsO(4) indeed show consistent activity and enantioselectivity in asymmetric dihydroxylation of olefins using K(3)Fe(CN)(6) and molecular oxygen as cooxidants. Compared to the Kobayashi heterogeneous systems, resin-OsO(4) is a very efficient catalyst for the dihydroxylation of a wide variety of aromatic, aliphatic, acyclic, cyclic, mono-, di-, and trisubstituted olefins to afford chiral vicinal diols with high yields and enantioselectivities irrespective of the cooxidant used. Resin-OsO(4) is recovered quantitatively by a simple filtration and reused for a number of cycles with consistent activity. The high binding ability of the heterogeneous osmium catalyst enables the use of an equimolar ratio of ligand to osmium to give excellent enantioselectives in asymmetric dihydroxylation in contrast to the homogeneous osmium system in which excess molar quantities of the expensive chiral ligand to osmium are invariably used. The complexation of the chiral ligand (DHQD)(2)PHAL, having very large dimension, a prerequisite to obtain higher ee, is possible only with the OsO(4)(2-) located on the surface of the supports.

Cell Chirality Drives Left-Right Asymmetric Morphogenesis.

Science.gov (United States)

Inaki, Mikiko; Sasamura, Takeshi; Matsuno, Kenji

2018-01-01

Most macromolecules found in cells are chiral, meaning that they cannot be superimposed onto their mirror image. However, cells themselves can also be chiral, a subject that has received little attention until very recently. In our studies on the mechanisms of left-right (LR) asymmetric development in Drosophila , we discovered that cells can have an intrinsic chirality to their structure, and that this "cell chirality" is generally responsible for the LR asymmetric development of certain organs in this species. The actin cytoskeleton plays important roles in the formation of cell chirality. In addition, Myosin31DF ( Myo31DF ), which encodes Drosophila Myosin ID, was identified as a molecular switch for cell chirality. In other invertebrate species, including snails and Caenorhabditis elegans , chirality of the blastomeres, another type of cell chirality, determines the LR asymmetry of structures in the body. Thus, chirality at the cellular level may broadly contribute to LR asymmetric development in various invertebrate species. Recently, cell chirality was also reported for various vertebrate cultured cells, and studies suggested that cell chirality is evolutionarily conserved, including the essential role of the actin cytoskeleton. Although the biological roles of cell chirality in vertebrates remain unknown, it may control LR asymmetric development or other morphogenetic events. The investigation of cell chirality has just begun, and this new field should provide valuable new insights in biology and medicine.

Use of nonlinear asymmetrical shock absorber to improve comfort on passenger vehicles

Science.gov (United States)

Silveira, M.; Pontes, B. R.; Balthazar, J. M.

2014-03-01

In this study the behaviour of two different types of shock absorbers, symmetrical (linear) and asymmetrical (nonlinear) is compared for use on passenger vehicles. The analyses use different standard road inputs and include variation of the severity parameter, the asymmetry ratio and the velocity of the vehicle. Performance indices and acceleration values are used to assess the efficacy of the asymmetrical systems. The comparisons show that the asymmetrical system, with nonlinear characteristics, tends to have a smoother and more progressive performance, both for vertical and angular movements. The half-car front asymmetrical system was introduced, and the simulation results show that the use of the asymmetrical system only at the front of the vehicle can further diminish the angular oscillations. As lower levels of acceleration are essential for improved ride comfort, the use of asymmetrical systems for vibrations and impact absorption can be a more advantageous choice for passenger vehicles.

Performance of JPEG Image Transmission Using Proposed Asymmetric Turbo Code

Directory of Open Access Journals (Sweden)

Siddiqi Mohammad Umar

2007-01-01

Full Text Available This paper gives the results of a simulation study on the performance of JPEG image transmission over AWGN and Rayleigh fading channels using typical and proposed asymmetric turbo codes for error control coding. The baseline JPEG algorithm is used to compress a QCIF ( "Suzie" image. The recursive systematic convolutional (RSC encoder with generator polynomials , that is, (13/11 in decimal, and 3G interleaver are used for the typical WCDMA and CDMA2000 turbo codes. The proposed asymmetric turbo code uses generator polynomials , that is, (13/11; 13/9 in decimal, and a code-matched interleaver. The effect of interleaver in the proposed asymmetric turbo code is studied using weight distribution and simulation. The simulation results and performance bound for proposed asymmetric turbo code for the frame length , code rate with Log-MAP decoder over AWGN channel are compared with the typical system. From the simulation results, it is observed that the image transmission using proposed asymmetric turbo code performs better than that with the typical system.

Hold your horSSEs: controlling structure-selective endonucleases MUS81 and Yen1/GEN1.

Science.gov (United States)

Blanco, Miguel G; Matos, Joao

2015-01-01

Repair of DNA lesions through homologous recombination promotes the establishment of stable chromosomal interactions. Multiple helicases, topoisomerases and structure-selective endonucleases (SSEs) act upon recombining joint molecules (JMs) to disengage chromosomal connections and safeguard chromosome segregation. Recent studies on two conserved SSEs - MUS81 and Yen1/GEN1- uncovered multiple layers of regulation that operate to carefully tailor JM-processing according to specific cellular needs. Temporal restriction of SSE function imposes a hierarchy in pathway usage that ensures efficient JM-processing while minimizing reciprocal exchanges between the recombining DNAs. Whereas a conserved strategy of fine-tuning SSE functions exists in different model systems, the precise molecular mechanisms to implement it appear to be significantly different. Here, we summarize the current knowledge on the cellular switches that are in place to control MUS81 and Yen1/GEN1 functions.

Establishment of a markerless mutation delivery system in Bacillus subtilis stimulated by a double-strand break in the chromosome.

Directory of Open Access Journals (Sweden)

Ting Shi

Full Text Available Bacillus subtilis has been a model for gram-positive bacteria and it has long been exploited for industrial and biotechnological applications. However, the availability of facile genetic tools for physiological analysis has generally lagged substantially behind traditional genetic models such as Escherichia coli and Saccharomyces cerevisiae. In this work, we have developed an efficient, precise and scarless method for rapid multiple genetic modifications without altering the chromosome of B. subtilis. This method employs upp gene as a counter-selectable marker, double-strand break (DSB repair caused by exogenous endonuclease I-SceI and comK overexpression for fast preparation of competent cell. Foreign dsDNA can be simply and efficiently integrated into the chromosome by double-crossover homologous recombination. The DSB repair is a potent inducement for stimulating the second intramolecular homologous recombination, which not only enhances the frequency of resolution by one to two orders of magnitude, but also selects for the resolved product. This method has been successfully and reiteratively used in B. subtilis to deliver point mutations, to generate in-frame deletions, and to construct large-scale deletions. Experimental results proved that it allowed repeated use of the selectable marker gene for multiple modifications and could be a useful technique for B. subtilis.

Asymmetric Modeling of the Industrial Heavy Water Plant (PIAP)

International Nuclear Information System (INIS)

Teruel, Federico; Aprea, J; Guido Lavalle, German

2000-01-01

Software of asymmetric stationary simulation for the Industrial Heavy Water Plant (PIAP) was developed, based on an existing symmetric simulator (Brigitte 2.0).This software allows to turn off some of the isotopic enrichment twin units present in the plant and to simulate them asymmetrically, in other words, with different selection of parameters between twins.Other incorporations were done, such as passing flows between units and entering flows in strategic points of the plant.The iterative system in which the symmetric simulator is based was insufficient to develop the asymmetric simulator, so the system was modeled according to an implicit scheme for the units that form the simulator.This type of resolution resulted in a simulator that supports a big range of boundary conditions and internal parameters.Moreover, the time of calculus is short (∼3 minutes), making it actually useful.The asymmetric simulator is at the PIAP now, for its study and validation. It shows expected tendencies and results according to the symmetric simulator already validated

Experimental and theoretical study on minimum achievable foil thickness during asymmetric rolling.

Directory of Open Access Journals (Sweden)

Delin Tang

Full Text Available Parts produced by microforming are becoming ever smaller. Similarly, the foils required in micro-machines are becoming ever thinner. The asymmetric rolling technique is capable of producing foils that are thinner than those produced by the conventional rolling technique. The difference between asymmetric rolling and conventional rolling is the 'cross-shear' zone. However, the influence of the cross-shear zone on the minimum achievable foil thickness during asymmetric rolling is still uncertain. In this paper, we report experiments designed to understand this critical influencing factor on the minimum achievable thickness in asymmetric rolling. Results showed that the minimum achievable thickness of rolled foils produced by asymmetric rolling with a rolling speed ratio of 1.3 can be reduced to about 30% of that possible by conventional rolling technique. Furthermore, the minimum achievable thickness during asymmetric rolling could be correlated to the cross-shear ratio, which, in turn, could be related to the rolling speed ratio. From the experimental results, a formula to calculate the minimum achievable thickness was established, considering the parameters cross-shear ratio, friction coefficient, work roll radius, etc. in asymmetric rolling.

Experimental and theoretical study on minimum achievable foil thickness during asymmetric rolling.

Science.gov (United States)

Tang, Delin; Liu, Xianghua; Song, Meng; Yu, Hailiang

2014-01-01

Parts produced by microforming are becoming ever smaller. Similarly, the foils required in micro-machines are becoming ever thinner. The asymmetric rolling technique is capable of producing foils that are thinner than those produced by the conventional rolling technique. The difference between asymmetric rolling and conventional rolling is the 'cross-shear' zone. However, the influence of the cross-shear zone on the minimum achievable foil thickness during asymmetric rolling is still uncertain. In this paper, we report experiments designed to understand this critical influencing factor on the minimum achievable thickness in asymmetric rolling. Results showed that the minimum achievable thickness of rolled foils produced by asymmetric rolling with a rolling speed ratio of 1.3 can be reduced to about 30% of that possible by conventional rolling technique. Furthermore, the minimum achievable thickness during asymmetric rolling could be correlated to the cross-shear ratio, which, in turn, could be related to the rolling speed ratio. From the experimental results, a formula to calculate the minimum achievable thickness was established, considering the parameters cross-shear ratio, friction coefficient, work roll radius, etc. in asymmetric rolling.

The theory of double layers

International Nuclear Information System (INIS)

Schamel, H.

1982-01-01

Numerical and in some degree laboratory experiments suggest the existence of at least two different kinds of time-independent double layers: a strictly monotonic transition of the electrostatic potential and a transition accompanied by a negative spike at the low potential side (ion acoustic DL). An interpretation of both is presented in terms of analytic BGK modes. The first class of DLs commonly observed in voltage- or beam-driven plasmas needs for its existence beam-type distributions satisfying a Bohm criterion. The potential drop is at least of the order of Tsub(e), and stability arguments favour currents which satisfy the Langmuir condition. The second class found in current-driven plasma simulations is correlated with ion holes. This latter kind of nonlinear wave-solutions is linearly based on the slow ion-acoustic mode and exists due to a vortex-like distortion of the ion distribution in the thermal range. During the growth of an ion hole which is triggered by ion-acoustic fluctuations, the partial reflection of streaming electrons causes different plasma states on both sides of the potential dip and makes the ion hole asymmetric giving rise to an effective potential drop. This implies that the amplitude of this second type of double layers has an upper limit of 1-2 Tsub(e) and presumes a temperature ratio of Tsub(e)/Tsub(i) > or approximately 3 in coincidence with the numerical results. (Auth.)

Asymmetric synthesis II more methods and applications

CERN Document Server

Christmann, Mathias

2012-01-01

After the overwhelming success of 'Asymmetric Synthesis - The Essentials', narrating the colorful history of asymmetric synthesis, this is the second edition with latest subjects and authors. While the aim of the first edition was mainly to honor the achievements of the pioneers in asymmetric syntheses, the aim of this new edition was bringing the current developments, especially from younger colleagues, to the attention of students. The format of the book remained unchanged, i.e. short conceptual overviews by young leaders in their field including a short biography of the authors. The growing multidisciplinary research within chemistry is reflected in the selection of topics including metal catalysis, organocatalysis, physical organic chemistry, analytical chemistry, and its applications in total synthesis. The prospective reader of this book is a graduate or undergraduate student of advanced organic chemistry as well as the industrial chemist who wants to get a brief update on the current developments in th...

Asymmetric Effects on Escape Rates of Bistable System

International Nuclear Information System (INIS)

Wang Canjun; Mei Dongcheng; Dai Zucheng

2011-01-01

The asymmetric effects on the escape rates from the stable states x ± in the bistable system are analyzed. The results indicate that the multiplicative noise and the additive noise always enhance the particle escape from stable states x ± of bistable. However, the asymmetric parameter r enhances the particle escape from stable state x + , and holds back the particle escape from stable state x - . (general)

Activation of a yeast replication origin near a double-stranded DNA break.

Science.gov (United States)

Raghuraman, M K; Brewer, B J; Fangman, W L

1994-03-01

Irradiation in the G1 phase of the cell cycle delays the onset of DNA synthesis and transiently inhibits the activation of replication origins in mammalian cells. It has been suggested that this inhibition is the result of the loss of torsional tension in the DNA after it has been damaged. Because irradiation causes DNA damage at an undefined number of nonspecific sites in the genome, it is not known how cells respond to limited DNA damage, and how replication origins in the immediate vicinity of a damage site would behave. Using the sequence-specific HO endonuclease, we have created a defined double-stranded DNA break in a centromeric plasmid in G1-arrested cells of the yeast Saccharomyces cerevisiae. We show that replication does initiate at the origin on the cut plasmid, and that the plasmid replicates early in the S phase after linearization in vivo. These observations suggest that relaxation of a supercoiled DNA domain in yeast need not inactivate replication origins within that domain. Furthermore, these observations rule out the possibility that the late replication context associated with chromosomal termini is a consequence of DNA ends.

Focused genetic recombination of bacteriophage t4 initiated by double-strand breaks.

Science.gov (United States)

Shcherbakov, Victor; Granovsky, Igor; Plugina, Lidiya; Shcherbakova, Tamara; Sizova, Svetlana; Pyatkov, Konstantin; Shlyapnikov, Michael; Shubina, Olga

2002-10-01

A model system for studying double-strand-break (DSB)-induced genetic recombination in vivo based on the ets1 segCDelta strain of bacteriophage T4 was developed. The ets1, a 66-bp DNA fragment of phage T2L containing the cleavage site for the T4 SegC site-specific endonuclease, was inserted into the proximal part of the T4 rIIB gene. Under segC(+) conditions, the ets1 behaves as a recombination hotspot. Crosses of the ets1 against rII markers located to the left and to the right of ets1 gave similar results, thus demonstrating the equal and symmetrical initiation of recombination by either part of the broken chromosome. Frequency/distance relationships were studied in a series of two- and three-factor crosses with other rIIB and rIIA mutants (all segC(+)) separated from ets1 by 12-2100 bp. The observed relationships were readily interpretable in terms of the modified splice/patch coupling model. The advantages of this localized or focused recombination over that distributed along the chromosome, as a model for studying the recombination-replication pathway in T4 in vivo, are discussed.

Diagnostic implications of asymmetrical mammographic patterns

International Nuclear Information System (INIS)

Asenjo, M.; Ania, B.J.

1997-01-01

To analyze the effect of asymmetrical mammographic patterns of the diagnosis of breast cancer. In a series of 6, 476 patients referred to a Breast Imaging Diagnosis Unit, we excluded males, women with previous breast surgery, and cases in which mammography was not performed, which left 5,203 women included. Each breast was classified according to one of four patterns of mammographic parenchymal density. Asymmetry was considered to exist when a patient's breasts had different patterns. Breast cancer was confirmed histologically in 282 (5.4%) women. The mammographic pattern was asymmetrical in 8% of the women with cancer and in 2% of the women without cancer (p<0.001). Fine-needle aspiration biopsy was performed in 78% and 96% (p=0.04), respectively, of the women with and without mammographic asymmetry who had neoplasms, and in 33% and 22% (p=0.02), respectively, of the women with and without mammographic asymmetry who did not have neoplasms. Asymmetrical mammographic pattern was four times more frequent in the women with breast cancer. This asymmetry decreased the frequency of needle biopsy in women with cancer, but increased the frequency of needle biopsy in women without cancer. (Author) 11 refs

Hadron scattering in an asymmetric box

International Nuclear Information System (INIS)

Li Xin; Chen Ying; Meng Guozhan; Feng Xu; Gong Ming; He Song; Li Gang; Liu Chuan; Liu Yubin; Ma Jianping; Meng Xiangfei; Shen Yan; Zhang Jianbo

2007-01-01

We propose to study hadron-hadron scattering using lattice QCD in an asymmetric box which allows one to access more non-degenerate low-momentum modes for a given volume. The conventional Luescher's formula applicable in a symmetric box is modified accordingly. To illustrate the feasibility of this approach, pion-pion elastic scattering phase shifts in the I = 2, J = 0 channel are calculated within quenched approximation using improved gauge and Wilson fermion actions on anisotropic lattices in an asymmetric box. After the chiral and continuum extrapolation, we find that our quenched results for the scattering phase shifts in this channel are consistent with the experimental data when the three-momentum of the pion is below 300MeV. Agreement is also found when compared with previous theoretical results from lattice and other means. Moreover, with the usage of asymmetric volume, we are able to compute the scattering phases in the low-momentum range (pion three momentum less than about 350MeV in the center of mass frame) for over a dozen values of the pion three-momenta, much more than using the conventional symmetric box with comparable volume

Uncovering the link between malfunctions in Drosophila neuroblast asymmetric cell division and tumorigenesis

Directory of Open Access Journals (Sweden)

Kelsom Corey

2012-11-01

Full Text Available Abstract Asymmetric cell division is a developmental process utilized by several organisms. On the most basic level, an asymmetric division produces two daughter cells, each possessing a different identity or fate. Drosophila melanogaster progenitor cells, referred to as neuroblasts, undergo asymmetric division to produce a daughter neuroblast and another cell known as a ganglion mother cell (GMC. There are several features of asymmetric division in Drosophila that make it a very complex process, and these aspects will be discussed at length. The cell fate determinants that play a role in specifying daughter cell fate, as well as the mechanisms behind setting up cortical polarity within neuroblasts, have proved to be essential to ensuring that neurogenesis occurs properly. The role that mitotic spindle orientation plays in coordinating asymmetric division, as well as how cell cycle regulators influence asymmetric division machinery, will also be addressed. Most significantly, malfunctions during asymmetric cell division have shown to be causally linked with neoplastic growth and tumor formation. Therefore, it is imperative that the developmental repercussions as a result of asymmetric cell division gone awry be understood.

Using Agent Based Distillation to Explore Issues Related to Asymmetric Warfare

Science.gov (United States)

2009-10-01

official definition of asymmetric warfare , considering that its use was redundant to irregular warfare [30]. 2 Such as the Lanchester Equations...RTP-MP-MSG-069 23 - 1 Using Agent Based Distillation to Explore Issues Related to Asymmetric Warfare Martin Adelantado, Jean-Michel Mathé...shows that both conventional and asymmetric warfare are characterised by nonlinear behaviours and that engagement is a Complex Adaptive System (CAS

Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

KAUST Repository

Rashid, Fahad

2017-02-23

Human flap endonuclease 1 (FEN1) and related structure-specific 5\\'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5\\'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually \\'locks\\' protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.

Controllable asymmetric transmission via gap-tunable acoustic metasurface

Science.gov (United States)

Liu, Bingyi; Jiang, Yongyuan

2018-04-01

In this work, we utilize the acoustic gradient metasurface (AGM) of a bilayer configuration to realize the controllable asymmetric transmission. Relying on the adjustable gap between the two composing layers, the metasurface could switch from symmetric transmission to asymmetric transmission at a certain gap value. The underlying mechanism is attributed to the interference between the forward diffracted waves scattered by the surface bound waves at two air-AGM interfaces, which is apparently influenced by the interlayer distance. We further utilize the hybrid acoustic elements to construct the desired gradient metasurface with a tunable gap and validate the controllable asymmetric transmission with full-wave simulations. Our work provides the solution for actively controlling the transmission property of an acoustic element, which shows potential application in acoustic communication as a dynamic tunable acoustic diode.

Study on the output factors of asymmetrical rectangular electron beam field

International Nuclear Information System (INIS)

Chen Yinghai; Yang Yueqin; Ma Yuhong; Zheng Jin; Zou Lijuan

2009-01-01

Objective: To evaluate the variant regularity of the output factors of asymmetrical rectangular electron beam field. Methods: The output factors of three special fields with different applicators and energies were measured by ionization chamber method at different off-axis distances. Then deviations of the output factors between asymmetrical and symmetric rectangular fields were calculated. Results: The changes of output factor with different off-axis distances in asymmetrical rectangular fields were basically consistent with those in standard square fields with the same applicator. It revealed that the output factor of asymmetrical rectangular field was related with the off-axis ratio of standard square field. Applicator and field size did not show obvious influence on the output factor. Conclusions: The output factor changes of asymmetrical rectangular field are mainly correlated with the off-axis ratio of standard square field. The correction of the output factor is determined by the off-axis ratio changes in standard square field. (authors)

Double-Skinned Forward Osmosis Membranes for Reducing Internal Concentration Polarization within the Porous Sublayer

KAUST Repository

Wang, Kai Yu

2010-05-19

A scheme to fabricate forward osmosis membranes comprising a highly porous sublayer sandwiched between two selective skin layers via phase inversion was proposed. One severe deficiency of existing composite and asymmetric membranes used in forward osmosis is the presence of unfavorable internal concentration polarization within the porous support layer that hinders both (i) separation (salt flux) and (ii) the performance (water flux). The double skin layers of the tailored membrane may mitigate the internal concentration polarization by preventing the salt and other solutes in the draw solution from penetrating into the membrane porous support. The prototype double-skinned cellulose acetate membrane displayed a water flux of 48.2 L·m-2·h -1 and lower reverse salt transport of 6.5 g·m -2·h-1 using 5.0 M MgCl2 as the draw solution in a forward osmosis process performed at 22 °C. This can be attributed to the effective salt rejection by the double skin layers and the low water transport resistance within the porous support layer. The prospects of utilizing the double-selective layer membranes may have potential application in forward osmosis for desalination. This study may help pave the way to improve the membrane design for the forward osmosis process. © 2010 American Chemical Society.

Double-Skinned Forward Osmosis Membranes for Reducing Internal Concentration Polarization within the Porous Sublayer

KAUST Repository

Wang, Kai Yu; Ong, Rui Chin; Chung, Tai-Shung

2010-01-01

A scheme to fabricate forward osmosis membranes comprising a highly porous sublayer sandwiched between two selective skin layers via phase inversion was proposed. One severe deficiency of existing composite and asymmetric membranes used in forward osmosis is the presence of unfavorable internal concentration polarization within the porous support layer that hinders both (i) separation (salt flux) and (ii) the performance (water flux). The double skin layers of the tailored membrane may mitigate the internal concentration polarization by preventing the salt and other solutes in the draw solution from penetrating into the membrane porous support. The prototype double-skinned cellulose acetate membrane displayed a water flux of 48.2 L·m-2·h -1 and lower reverse salt transport of 6.5 g·m -2·h-1 using 5.0 M MgCl2 as the draw solution in a forward osmosis process performed at 22 °C. This can be attributed to the effective salt rejection by the double skin layers and the low water transport resistance within the porous support layer. The prospects of utilizing the double-selective layer membranes may have potential application in forward osmosis for desalination. This study may help pave the way to improve the membrane design for the forward osmosis process. © 2010 American Chemical Society.

Success Factors of Asymmetric Connections - Example of Large Slovenian Enterprises

Directory of Open Access Journals (Sweden)

Viktor Vračar

2014-11-01

Full Text Available More and more companies realize the fact that networking or partner collaborations, which are based on partner relations between companies, are essential for their long-term existence. In today’s global competitive environment each company is included at least in some different connections. Very common connections occur between large and smaller enterprises, where the so called asymmetric connections occur, which may be understood as the ability of one organisation to establish power, influence and control over the other organisation and its resources. According to numerous statements, the connections between enterprises are very frequently uneffectivenessful, with opinions on the optimal nature of asymmetric connections being quite common as well, whereby it is, as a rule, a synergic complementing of missing content for both partners. To verify the thesis, that companies achieve more competitiveness and effectiveness through connections, whereby the so called asymmetric connections are common, a structural model of the evolution of asymmetric connection has been developed, which connects the theoretically identified factors and all dependent concepts of competitiveness, efficiency and effectiveness. The empirical research also attempts to further expose the factors of asymmetric connections, which affect efficiency and effectiveness of the connected enterprises.

Symmetrization of the beam-beam interaction in an asymmetric collider

International Nuclear Information System (INIS)

Chin, Y.H.

1990-07-01

This paper studies the idea of symmetrizing both the lattice and the beams of an asymmetric collider, and discusses why this regime should be within the parametric reach of the design in order to credibly ensure its performance. Also examined is the effectiveness of a simple compensation method using the emittance as a free parameter and that it does not work in all cases. At present, when there are no existing asymmetric colliders, it seems prudent to design an asymmetric collider so as to be similar to a symmetric one (without relying on a particular theory of the asymmetric beam-beam interaction that has not passed tests of fidelity). Nevertheless, one must allow for the maximum possible flexibility and freedom in adjusting those parameters that affect luminosity. Such a parameter flexibility will be essential in tuning the collider to the highest luminosity

Force on an Asymmetric Capacitor

National Research Council Canada - National Science Library

Bahder, Thomas

2003-01-01

.... At present, the physical basis for the Biefeld-Brown effect is not understood. The order of magnitude of the net force on the asymmetric capacitor is estimated assuming two different mechanisms of charge conduction between its electrodes...

The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once.

Science.gov (United States)

Tsutakawa, Susan E; Lafrance-Vanasse, Julien; Tainer, John A

2014-07-01

To avoid genome instability, DNA repair nucleases must precisely target the correct damaged substrate before they are licensed to incise. Damage identification is a challenge for all DNA damage response proteins, but especially for nucleases that cut the DNA and necessarily create a cleaved DNA repair intermediate, likely more toxic than the initial damage. How do these enzymes achieve exquisite specificity without specific sequence recognition or, in some cases, without a non-canonical DNA nucleotide? Combined structural, biochemical, and biological analyses of repair nucleases are revealing their molecular tools for damage verification and safeguarding against inadvertent incision. Surprisingly, these enzymes also often act on RNA, which deserves more attention. Here, we review protein-DNA structures for nucleases involved in replication, base excision repair, mismatch repair, double strand break repair (DSBR), and telomere maintenance: apurinic/apyrimidinic endonuclease 1 (APE1), Endonuclease IV (Nfo), tyrosyl DNA phosphodiesterase (TDP2), UV Damage endonuclease (UVDE), very short patch repair endonuclease (Vsr), Endonuclease V (Nfi), Flap endonuclease 1 (FEN1), exonuclease 1 (Exo1), RNase T and Meiotic recombination 11 (Mre11). DNA and RNA structure-sensing nucleases are essential to life with roles in DNA replication, repair, and transcription. Increasingly these enzymes are employed as advanced tools for synthetic biology and as targets for cancer prognosis and interventions. Currently their structural biology is most fully illuminated for DNA repair, which is also essential to life. How DNA repair enzymes maintain genome fidelity is one of the DNA double helix secrets missed by James Watson and Francis Crick, that is only now being illuminated though structural biology and mutational analyses. Structures reveal motifs for repair nucleases and mechanisms whereby these enzymes follow the old carpenter adage: measure twice, cut once. Furthermore, to measure

Double peak-induced distance error in short-time-Fourier-transform-Brillouin optical time domain reflectometers event detection and the recovery method.

Science.gov (United States)

Yu, Yifei; Luo, Linqing; Li, Bo; Guo, Linfeng; Yan, Jize; Soga, Kenichi

2015-10-01

The measured distance error caused by double peaks in the BOTDRs (Brillouin optical time domain reflectometers) system is a kind of Brillouin scattering spectrum (BSS) deformation, discussed and simulated for the first time in the paper, to the best of the authors' knowledge. Double peak, as a kind of Brillouin spectrum deformation, is important in the enhancement of spatial resolution, measurement accuracy, and crack detection. Due to the variances of the peak powers of the BSS along the fiber, the measured starting point of a step-shape frequency transition region is shifted and results in distance errors. Zero-padded short-time-Fourier-transform (STFT) can restore the transition-induced double peaks in the asymmetric and deformed BSS, thus offering more accurate and quicker measurements than the conventional Lorentz-fitting method. The recovering method based on the double-peak detection and corresponding BSS deformation can be applied to calculate the real starting point, which can improve the distance accuracy of the STFT-based BOTDR system.

Asymmetric synthesis of cyclo-archaeol and ß-glucosyl cyclo-archaeol

NARCIS (Netherlands)

Ferrer, C.; Fodran, P.; Barroso, S.; Gibson, R.; Hopmans, E.C.; Sinninghe Damsté, J.S.; Schouten, S.; Minnaard, A.J.

2013-01-01

An efficient asymmetric synthesis of cyclo-archaeol and beta-glucosyl cyclo-archaeol is presented employing catalytic asymmetric conjugate addition and catalytic epoxide ring opening as the key steps. Their occurrence in deep sea hydrothermal vents has been confirmed by chromatographic comparison

Asymmetric Damage Segregation Constitutes an Emergent Population-Level Stress Response

DEFF Research Database (Denmark)

Vedel, Søren; Nunns, Harry; Košmrlj, Andrej

2016-01-01

Asymmetric damage segregation (ADS) is a mechanism for increasing population fitness through non-random, asymmetric partitioning of damaged macromolecules at cell division. ADS has been reported across multiple organisms, though the measured effects on fitness of individuals are often small. Here...

Modulational Instability in Linearly Coupled Asymmetric Dual-Core Fibers

Directory of Open Access Journals (Sweden)

Arjunan Govindarajan

2017-06-01

Full Text Available We investigate modulational instability (MI in asymmetric dual-core nonlinear directional couplers incorporating the effects of the differences in effective mode areas and group velocity dispersions, as well as phase- and group-velocity mismatches. Using coupled-mode equations for this system, we identify MI conditions from the linearization with respect to small perturbations. First, we compare the MI spectra of the asymmetric system and its symmetric counterpart in the case of the anomalous group-velocity dispersion (GVD. In particular, it is demonstrated that the increase of the inter-core linear-coupling coefficient leads to a reduction of the MI gain spectrum in the asymmetric coupler. The analysis is extended for the asymmetric system in the normal-GVD regime, where the coupling induces and controls the MI, as well as for the system with opposite GVD signs in the two cores. Following the analytical consideration of the MI, numerical simulations are carried out to explore nonlinear development of the MI, revealing the generation of periodic chains of localized peaks with growing amplitudes, which may transform into arrays of solitons.

Effects of asymmetrical stance and movement on body rotation in pushing.

Science.gov (United States)

Lee, Yun-Ju; Aruin, Alexander S

2015-01-21

Pushing objects in the presence of body asymmetries could increase the risk of back injury. Furthermore, when the object is heavy, it could exacerbate the effects induced by asymmetrical posture. We investigated how the use of asymmetrical posture and/or upper extremity movement affect vertical torque (Tz) and center of pressure (COP) displacement during pushing. Ten healthy volunteers were instructed to push objects of three different weights using two hands (symmetrical hand use) or one hand (asymmetrical hand use) while standing in symmetrical or asymmetrical foot-positions. The peak values of Tz and COP displacement in the medial-lateral direction (COPML) were analyzed. In cases of isolated asymmetry, changes in the Tz were mainly linked with effects of hand-use whereas effects of foot-position dominated changes in the COPML displacement. In cases of a combined asymmetry, the magnitudes of both Tz and COPML were additive when asymmetrical hand-use and foot-position induced the rotation of the lower and upper body in the same direction or subtractive when asymmetries resulted in the rotation of the body segments in the opposite directions. Moreover, larger Tz and COP displacements were seen when pushing the heavy weight. The results point out the importance of using Tz and COPML to describe the isolated or combined effects of asymmetrical upper extremity movement and asymmetrical posture on body rotation during pushing. Furthermore, it suggests that a proper combination of unilateral arm movement and foot placements could help to reduce body rotation even when pushing heavy objects. Copyright © 2014 Elsevier Ltd. All rights reserved.

Asymmetric underlap optimization of sub-10nm finfets for realizing energy-efficient logic and robust memories

Science.gov (United States)

Akkala, Arun Goud

Leakage currents in CMOS transistors have risen dramatically with technology scaling leading to significant increase in standby power consumption. Among the various transistor candidates, the excellent short channel immunity of Silicon double gate FinFETs have made them the best contender for successful scaling to sub-10nm nodes. For sub-10nm FinFETs, new quantum mechanical leakage mechanisms such as direct source to drain tunneling (DSDT) of charge carriers through channel potential energy barrier arising due to proximity of source/drain regions coupled with the high transport direction electric field is expected to dominate overall leakage. To counter the effects of DSDT and worsening short channel effects and to maintain Ion/ Ioff, performance and power consumption at reasonable values, device optimization techniques are necessary for deeply scaled transistors. In this work, source/drain underlapping of FinFETs has been explored using quantum mechanical device simulations as a potentially promising method to lower DSDT while maintaining the Ion/ Ioff ratio at acceptable levels. By adopting a device/circuit/system level co-design approach, it is shown that asymmetric underlapping, where the drain side underlap is longer than the source side underlap, results in optimal energy efficiency for logic circuits in near-threshold as well as standard, super-threshold operating regimes. In addition, read/write conflict in 6T SRAMs and the degradation in cell noise margins due to the low supply voltage can be mitigated by using optimized asymmetric underlapped n-FinFETs for the access transistor, thereby leading to robust cache memories. When gate-workfunction tuning is possible, using asymmetric underlapped n-FinFETs for both access and pull-down devices in an SRAM bit cell can lead to high-speed and low-leakage caches. Further, it is shown that threshold voltage degradation in the presence of Hot Carrier Injection (HCI) is less severe in asymmetric underlap n-FinFETs. A

Project financing versus corporate financing under asymmetric information

OpenAIRE

Anton Miglo

2008-01-01

In recent years financing through the creation of an independent project company or financing by non-recourse debt has become an important part of corporate decisions. Shah and Thakor (JET, 1987) argue that project financing can be optimal when asymmetric information exists between firm's insiders and market participants. In contrast to that paper, we provide an asymmetric information argument for project financing without relying on corporate taxes, costly information production or an assump...

Asymmetric Shaped-Pattern Synthesis for Planar Antenna Arrays

Directory of Open Access Journals (Sweden)

T. M. Bruintjes

2016-01-01

Full Text Available A procedure to synthesize asymmetrically shaped beam patterns is developed for planar antenna arrays. As it is based on the quasi-analytical method of collapsed distributions, the main advantage of this procedure is the ability to realize a shaped (null-free region with very low ripple. Smooth and asymmetrically shaped regions can be used for Direction-of-Arrival estimation and subsequently for efficient tracking with a single output (fully analog beamformer.

Asymmetric collider

International Nuclear Information System (INIS)

Bharadwaj, V.; Colestock, P.; Goderre, G.; Johnson, D.; Martin, P.; Holt, J.; Kaplan, D.

1993-01-01

The study of CP violation in beauty decay is one of the key challenges facing high energy physics. Much work has not yielded a definitive answer how this study might best be performed. However, one clear conclusion is that new accelerator facilities are needed. Proposals include experiments at asymmetric electron-positron colliders and in fixed-target and collider modes at LHC and SSC. Fixed-target and collider experiments at existing accelerators, while they might succeed in a first observation of the effect, will not be adequate to study it thoroughly. Giomataris has emphasized the potential of a new approach to the study of beauty CP violation: the asymmetric proton collider. Such a collider might be realized by the construction of a small storage ring intersecting an existing or soon-to-exist large synchrotron, or by arranging collisions between a large synchrotron and its injector. An experiment at such a collider can combine the advantages of fixed-target-like spectrometer geometry, facilitating triggering, particle identification and the instrumentation of a large acceptance, while the increased √s can provide a factor > 100 increase in beauty-production cross section compared to Tevatron or HERA fixed-target. Beams crossing at a non-zero angle can provide a small interaction region, permitting a first-level decay-vertex trigger to be implemented. To achieve large √s with a large Lorentz boost and high luminosity, the most favorable venue is the high-energy booster (HEB) at the SSC Laboratory, though the CERN SPS and Fermilab Tevatron are also worth considering

An Evolving Asymmetric Game for Modeling Interdictor-Smuggler Problems

Science.gov (United States)

2016-06-01

ASYMMETRIC GAME FOR MODELING INTERDICTOR-SMUGGLER PROBLEMS by Richard J. Allain June 2016 Thesis Advisor: David L. Alderson Second Reader: W...DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE AN EVOLVING ASYMMETRIC GAME FOR MODELING INTERDICTOR- SMUGGLER PROBLEMS 5. FUNDING NUMBERS 6...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release; distribution is unlimited AN EVOLVING

DNA double-strand break measurement in mammalian cells by pulsed-field gel electrophoresis: an approach using restriction enzymes and gene probing

International Nuclear Information System (INIS)

Loebrich, M.; Ikpeme, S.; Kiefer, J.

1994-01-01

DNA samples prepared from human SP 3 cells, which had not been exposed to various doses of X-ray, were treated with NotI restriction endonuclease before being run in a contour-clamped homogeneous electrophoresis system. The restriction enzyme cuts the DNA at defined positions delivering DNA sizes which can be resolved by pulsed-field gel electrophoresis (PFGE). In order to investigate only one of the DNA fragments, a human lactoferrin cDNA, pHL-41, was hybridized to the DNA separated by PFGE. As a result, only the DNA fragment which contains the hybridized gene was detected resulting in a one-band pattern. The decrease of this band was found to be exponential with increasing radiation dose. From the slope, a double-strand break induction rate of (6.3±0.7) x 10 -3 /Mbp/Gy was deduced for 80 kV X-rays. (Author)

Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP Assay for the Detection of Bacterial Meningitis Pathogens

Directory of Open Access Journals (Sweden)

Owen Higgins

2018-02-01

Full Text Available Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae. Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae, N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology.

Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens

Science.gov (United States)

Clancy, Eoin; Cormican, Martin; Boo, Teck Wee; Cunney, Robert

2018-01-01

Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae. Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae, N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology. PMID:29425124

Asymmetric Penning trap coherent states

International Nuclear Information System (INIS)

Contreras-Astorga, Alonso; Fernandez, David J.

2010-01-01

By using a matrix technique, which allows to identify directly the ladder operators, the coherent states of the asymmetric Penning trap are derived as eigenstates of the appropriate annihilation operators. They are compared with those obtained through the displacement operator method.

Asymmetric threat data mining and knowledge discovery

Science.gov (United States)

Gilmore, John F.; Pagels, Michael A.; Palk, Justin

2001-03-01

Asymmetric threats differ from the conventional force-on- force military encounters that the Defense Department has historically been trained to engage. Terrorism by its nature is now an operational activity that is neither easily detected or countered as its very existence depends on small covert attacks exploiting the element of surprise. But terrorism does have defined forms, motivations, tactics and organizational structure. Exploiting a terrorism taxonomy provides the opportunity to discover and assess knowledge of terrorist operations. This paper describes the Asymmetric Threat Terrorist Assessment, Countering, and Knowledge (ATTACK) system. ATTACK has been developed to (a) data mine open source intelligence (OSINT) information from web-based newspaper sources, video news web casts, and actual terrorist web sites, (b) evaluate this information against a terrorism taxonomy, (c) exploit country/region specific social, economic, political, and religious knowledge, and (d) discover and predict potential terrorist activities and association links. Details of the asymmetric threat structure and the ATTACK system architecture are presented with results of an actual terrorist data mining and knowledge discovery test case shown.

Hybrid cryptosystem for image file using elgamal and double playfair cipher algorithm

Science.gov (United States)

Hardi, S. M.; Tarigan, J. T.; Safrina, N.

2018-03-01

In this paper, we present an implementation of an image file encryption using hybrid cryptography. We chose ElGamal algorithm to perform asymmetric encryption and Double Playfair for the symmetric encryption. Our objective is to show that these algorithms are capable to encrypt an image file with an acceptable running time and encrypted file size while maintaining the level of security. The application was built using C# programming language and ran as a stand alone desktop application under Windows Operating System. Our test shows that the system is capable to encrypt an image with a resolution of 500×500 to a size of 976 kilobytes with an acceptable running time.

Chiral 1,3,2-oxazaborolidines in asymmetric synthesis: recent advances

International Nuclear Information System (INIS)

Glushkov, Vladimir A; Tolstikov, Alexander G

2004-01-01

The use of chiral 1,3,2-oxazaborolidines in asymmetric organic synthesis, particularly, in enantioselective reduction of ketones, imines and oxime ethers, asymmetric Diels-Alder reactions, aldol condensation and atroposelective reduction of lactones is reviewed. Reactions of immobilised 1,3,2-oxazaborolidines are also considered.

Universal Critical Power for Nonlinear Schroedinger Equations with a Symmetric Double Well Potential

International Nuclear Information System (INIS)

Sacchetti, Andrea

2009-01-01

Here we consider stationary states for nonlinear Schroedinger equations in any spatial dimension n with symmetric double well potentials. These states may bifurcate as the strength of the nonlinear term increases and we observe two different pictures depending on the value of the nonlinearity power: a supercritical pitchfork bifurcation, and a subcritical pitchfork bifurcation with two asymmetric branches occurring as the result of saddle-node bifurcations. We show that in the semiclassical limit, or for a large barrier between the two wells, the first kind of bifurcation always occurs when the nonlinearity power is less than a critical value; in contrast, when the nonlinearity power is larger than such a critical value then we always observe the second scenario. The remarkable fact is that such a critical value is a universal constant in the sense that it does not depend on the shape of the double well potential and on the dimension n.

Holding-time-aware asymmetric spectrum allocation in virtual optical networks

Science.gov (United States)

Lyu, Chunjian; Li, Hui; Liu, Yuze; Ji, Yuefeng

2017-10-01

Virtual optical networks (VONs) have been considered as a promising solution to support current high-capacity dynamic traffic and achieve rapid applications deployment. Since most of the network services (e.g., high-definition video service, cloud computing, distributed storage) in VONs are provisioned by dedicated data centers, needing different amount of bandwidth resources in both directions, the network traffic is mostly asymmetric. The common strategy, symmetric provisioning of traffic in optical networks, leads to a waste of spectrum resources in such traffic patterns. In this paper, we design a holding-time-aware asymmetric spectrum allocation module based on SDON architecture and an asymmetric spectrum allocation algorithm based on the module is proposed. For the purpose of reducing spectrum resources' waste, the algorithm attempts to reallocate the idle unidirectional spectrum slots in VONs, which are generated due to the asymmetry of services' bidirectional bandwidth. This part of resources can be exploited by other requests, such as short-time non-VON requests. We also introduce a two-dimensional asymmetric resource model for maintaining idle spectrum resources information of VON in spectrum and time domains. Moreover, a simulation is designed to evaluate the performance of the proposed algorithm, and results show that our proposed asymmetric spectrum allocation algorithm can improve the resource waste and reduce blocking probability.

Asymmetric Price Transmission in Indonesia's Wheat Flour Market

OpenAIRE

Varela, Gonzalo J.; Taniguchi, Kiyoshi

2014-01-01

Data indicate that its domestic price in Indonesia has been increasing regardless of movements in the international price of wheat. A test for asymmetric price transmission from international wheat to domestic wheat flour markets is conducted using an error correction model and find the presence of asymmetric price transmission. The upward adjustment in the domestic price of wheat flour is much faster than its adjustment downward when it deviates from long-run equilibrium. Our results are rob...

Detection of endonuclease III- and 8-oxoguanine glycosylase-sensitive base modifications in γ-irradiated DNA and cells by the aldehyde reactive probe (ARP) assay

International Nuclear Information System (INIS)

Mohsin Ali, M.; Kurisu, Satofumi; Yoshioka, Yoshihiro; Terato, Hiroaki; Ohyama, Yoshihiko; Ide Hiroshi; Kubo, Kihei

2004-01-01

Ionizing radiation generates diverse DNA lesions that differentially induce cell death and mutations. In the present study, calf thymus DNA (400 μg/ml) and HeLa cells were irradiated by 60 Co γ-rays, and abasic (AP) sites and endonuclease (Endo) III- and 8-oxoguanine glycosylase (hOGG1)-sensitive base modifications in DNA were quantitated by the aldehyde reactive probe (ARP) assay. The irradiation of calf thymus DNA in phosphate buffer generated 91 Endo III- and 100 hOGG1-sensitive base modifications and 110 AP sites per 10 6 base pairs (bp) per Gy. The yield of the lesions in Tris buffer was 41- to 91-fold lower than that in phosphate, demonstrating a radioprotective effect of Tris. The HeLa cell chromosomal DNA contained 12 Endo III- and 3.8 hOGG1-sensitive base modifications and less than 1 AP sites per 10 6 bp as endogenous damage, and their level was increased by irradiation. The yields of the damage at 1 Gy (roughly equivalent to the lethal dose of HeLa cells [1.6-1.8 Gy]) were 0.13 Endo III, 0.091 hOGG1, and 0.065 AP sites per 10 6 bp, showing that irradiation with a lethal dose brought about only a marginal increase in base damage relative to an endogenous one. A comparison of the present data with those reported for DNA strand breaks supports the primary importance of double-strand breaks and clustered lesions as lethal damages formed by ionizing radiation. (author)

Asymmetrical Capacitors for Propulsion and the ISR Asymmetrical Capacitator Thruster, Experimental Results and Improved Designs

Science.gov (United States)

Canning, Francis; Winet, Ed; Ice, Bob; Melcher, Cory; Pesavento, Phil; Holmes, Alan; Butler, Carey; Cole, John; Campbell, Jonathan

2004-01-01

The outline of this viewgraph presentation on asymmetrical capacitor thruster development includes: 1) Test apparatus; 2) Devices tested; 3) Circuits used; 4) Data collected (Time averaged, Time resolved); 5) Patterns observed; 6) Force calculation; 7) Electrostatic modeling; 8) Understand it all.

From design to manufacturing of asymmetric teeth gears using computer application

Science.gov (United States)

Suciu, F.; Dascalescu, A.; Ungureanu, M.

2017-05-01

The asymmetric cylindrical gears, with involutes teeth profiles having different base circle diameters, are nonstandard gears, used with the aim to obtain better function parameters for the active profile. We will expect that the manufacturing of these gears became possible only after the design and realization of some specific tools. The paper present how the computer aided design and applications developed in MATLAB, for obtain the geometrical parameters, in the same time for calculation some functional parameters like stress and displacements, transmission error, efficiency of the gears and the 2D models, generated with AUTOLISP applications, are used for computer aided manufacturing of asymmetric gears with standard tools. So the specific tools considered one of the disadvantages of these gears are not necessary and implicitly the expected supplementary costs are reduced. The calculus algorithm established for the asymmetric gear design application use the „direct design“ of the spur gears. This method offers the possibility of determining first the parameters of the gears, followed by the determination of the asymmetric gear rack’s parameters, based on those of the gears. Using original design method and computer applications have been determined the geometrical parameters, the 2D and 3D models of the asymmetric gears and on the base of these models have been manufacturing on CNC machine tool asymmetric gears.

Colossal enhancement in thermoelectric effect in a laterally coupled double-quantum-dot chain by the Coulomb interactions

International Nuclear Information System (INIS)

Xiong, Lun; Yi, Lin

2014-01-01

Thermoelectric effects, including Seebeck coefficient (S), thermal conductance (κ), and figure of merit (ZT), in a laterally coupled double-quantum-dot (DQD) chain with two external nonmagnetic contacts are investigated theoretically by the nonequilibrium Green's function formalism. In this system, the DQD chain between two contacts forms a main channel for thermal electrons transporting, and each QD in the main chain couples laterally to a dangling one. The numerical calculations show that the Coulomb interactions not only lead to the splitting of the asymmetrical double-peak structure of the Seebeck coefficient, but also make the thermal spectrum show a strong violation of the Wiedemann–Franz law, leading to a colossal enhancement in ZT. These results indicate that the coupled DQD chain has potential applications in the thermoelectric devices with high thermal efficiency.

Totally Asymmetric Limit for Models of Heat Conduction

Science.gov (United States)

De Carlo, Leonardo; Gabrielli, Davide

2017-08-01

We consider one dimensional weakly asymmetric boundary driven models of heat conduction. In the cases of a constant diffusion coefficient and of a quadratic mobility we compute the quasi-potential that is a non local functional obtained by the solution of a variational problem. This is done using the dynamic variational approach of the macroscopic fluctuation theory (Bertini et al. in Rev Mod Phys 87:593, 2015). The case of a concave mobility corresponds essentially to the exclusion model that has been discussed in Bertini et al. (J Stat Mech L11001, 2010; Pure Appl Math 64(5):649-696, 2011; Commun Math Phys 289(1):311-334, 2009) and Enaud and Derrida (J Stat Phys 114:537-562, 2004). We consider here the convex case that includes for example the Kipnis-Marchioro-Presutti (KMP) model and its dual (KMPd) (Kipnis et al. in J Stat Phys 27:6574, 1982). This extends to the weakly asymmetric regime the computations in Bertini et al. (J Stat Phys 121(5/6):843-885, 2005). We consider then, both microscopically and macroscopically, the limit of large externalfields. Microscopically we discuss some possible totally asymmetric limits of the KMP model. In one case the totally asymmetric dynamics has a product invariant measure. Another possible limit dynamics has instead a non trivial invariant measure for which we give a duality representation. Macroscopically we show that the quasi-potentials of KMP and KMPd, which are non local for any value of the external field, become local in the limit. Moreover the dependence on one of the external reservoirs disappears. For models having strictly positive quadratic mobilities we obtain instead in the limit a non local functional having a structure similar to the one of the boundary driven asymmetric exclusion process.

High-Stacking-Density, Superior-Roughness LDH Bridged with Vertically Aligned Graphene for High-Performance Asymmetric Supercapacitors.

Science.gov (United States)

Guo, Wei; Yu, Chang; Li, Shaofeng; Yang, Juan; Liu, Zhibin; Zhao, Changtai; Huang, Huawei; Zhang, Mengdi; Han, Xiaotong; Niu, Yingying; Qiu, Jieshan

2017-10-01

The high-performance electrode materials with tuned surface and interface structure and functionalities are highly demanded for advanced supercapacitors. A novel strategy is presented to conFigure high-stacking-density, superior-roughness nickel manganese layered double hydroxide (LDH) bridged by vertically aligned graphene (VG) with nickel foam (NF) as the conductive collector, yielding the LDH-NF@VG hybrids for asymmetric supercapacitors. The VG nanosheets provide numerous electron transfer channels for quick redox reactions, and well-developed open structure for fast mass transport. Moreover, the high-stacking-density LDH grown and assembled on VG nanosheets result in a superior hydrophilicity derived from the tuned nano/microstructures, especially microroughness. Such a high stacking density with abundant active sites and superior wettability can be easily accessed by aqueous electrolytes. Benefitting from the above features, the LDH-NF@VG can deliver a high capacitance of 2920 F g -1 at a current density of 2 A g -1 , and the asymmetric supercapacitor with the LDH-NF@VG as positive electrode and activated carbon as negative electrode can deliver a high energy density of 56.8 Wh kg -1 at a power density of 260 W kg -1 , with a high specific capacitance retention rate of 87% even after 10 000 cycles. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A new restriction endonuclease-based method for highly-specific detection of DNA targets from methicillin-resistant Staphylococcus aureus.

Directory of Open Access Journals (Sweden)

Maria W Smith

Full Text Available PCR multiplexing has proven to be challenging, and thus has provided limited means for pathogen genotyping. We developed a new approach for analysis of PCR amplicons based on restriction endonuclease digestion. The first stage of the restriction enzyme assay is hybridization of a target DNA to immobilized complementary oligonucleotide probes that carry a molecular marker, horseradish peroxidase (HRP. At the second stage, a target-specific restriction enzyme is added, cleaving the target-probe duplex at the corresponding restriction site and releasing the HRP marker into solution, where it is quantified colorimetrically. The assay was tested for detection of the methicillin-resistant Staphylococcus aureus (MRSA pathogen, using the mecA gene as a target. Calibration curves indicated that the limit of detection for both target oligonucleotide and PCR amplicon was approximately 1 nM. Sequences of target oligonucleotides were altered to demonstrate that (i any mutation of the restriction site reduced the signal to zero; (ii double and triple point mutations of sequences flanking the restriction site reduced restriction to 50-80% of the positive control; and (iii a minimum of a 16-bp target-probe dsDNA hybrid was required for significant cleavage. Further experiments showed that the assay could detect the mecA amplicon from an unpurified PCR mixture with detection limits similar to those with standard fluorescence-based qPCR. Furthermore, addition of a large excess of heterologous genomic DNA did not affect amplicon detection. Specificity of the assay is very high because it involves two biorecognition steps. The proposed assay is low-cost and can be completed in less than 1 hour. Thus, we have demonstrated an efficient new approach for pathogen detection and amplicon genotyping in conjunction with various end-point and qPCR applications. The restriction enzyme assay may also be used for parallel analysis of multiple different amplicons from the same

Best Speed Fit EDF Scheduling for Performance Asymmetric Multiprocessors

Directory of Open Access Journals (Sweden)

Peng Wu

2017-01-01

Full Text Available In order to improve the performance of a real-time system, asymmetric multiprocessors have been proposed. The benefits of improved system performance and reduced power consumption from such architectures cannot be fully exploited unless suitable task scheduling and task allocation approaches are implemented at the operating system level. Unfortunately, most of the previous research on scheduling algorithms for performance asymmetric multiprocessors is focused on task priority assignment. They simply assign the highest priority task to the fastest processor. In this paper, we propose BSF-EDF (best speed fit for earliest deadline first for performance asymmetric multiprocessor scheduling. This approach chooses a suitable processor rather than the fastest one, when allocating tasks. With this proposed BSF-EDF scheduling, we also derive an effective schedulability test.

Gravity-induced asymmetric distribution of a plant growth hormone

Science.gov (United States)

Bandurski, R. S.; Schulze, A.; Momonoki, Y.

1984-01-01

Dolk (1936) demonstrated that gravistimulation induced an asymmetric distribution of auxin in a horizontally-placed shoot. An attempt is made to determine where and how that asymmetry arises, and to demonstrate that the endogenous auxin, indole-3-acetic acid, becomes asymmetrically distributed in the cortical cells of the Zea mays mesocotyl during 3 min of geostimulation. Further, indole-3-acetic acid derived by hydrolysis of an applied transport form of the hormone, indole-3-acetyl-myo-inositol, becomes asymmetrically distributed within 15 min of geostimulus time. From these and prior data is developed a working theory that the gravitational stimulus induces a selective leakage, or secretion, of the hormone from the vascular tissue to the cortical cells of the mesocotyl.

Asymmetric acoustic transmission in multiple frequency bands

Energy Technology Data Exchange (ETDEWEB)

Sun, Hong-xiang, E-mail: jsdxshx@ujs.edu.cn [Research Center of Fluid Machinery Engineering and Technology, Jiangsu University, Zhenjiang 212013 (China); Laboratory of Modern Acoustics, Institute of Acoustics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 (China); State Key Laboratory of Acoustics, Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190 (China); Yuan, Shou-qi, E-mail: Shouqiy@ujs.edu.cn [Research Center of Fluid Machinery Engineering and Technology, Jiangsu University, Zhenjiang 212013 (China); Zhang, Shu-yi [Laboratory of Modern Acoustics, Institute of Acoustics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 (China)

2015-11-23

We report both experimentally and numerically that the multi-band device of the asymmetric acoustic transmission is realized by placing two periodic gratings with different periods on both sides of two brass plates immersed in water. The asymmetric acoustic transmission can exist in four frequency bands below 1500 kHz, which arises from the interaction between various diffractions from the two gratings and Lamb modes in the brass plates immersed in water. The results indicate that the device has the advantages of multiple band, broader bandwidth, and simpler structure. Our finding should have great potential applications in ultrasonic devices.

Asymmetric acoustic transmission in multiple frequency bands

International Nuclear Information System (INIS)

Sun, Hong-xiang; Yuan, Shou-qi; Zhang, Shu-yi

2015-01-01

We report both experimentally and numerically that the multi-band device of the asymmetric acoustic transmission is realized by placing two periodic gratings with different periods on both sides of two brass plates immersed in water. The asymmetric acoustic transmission can exist in four frequency bands below 1500 kHz, which arises from the interaction between various diffractions from the two gratings and Lamb modes in the brass plates immersed in water. The results indicate that the device has the advantages of multiple band, broader bandwidth, and simpler structure. Our finding should have great potential applications in ultrasonic devices

The asymmetric total synthesis of (+)- and (-)-trypargine via Noyori asymmetric transfer hydrogenation

International Nuclear Information System (INIS)

Pilli, Ronaldo A.; Rodrigues Junior, Manoel Trindade

2009-01-01

A concise and efficient total synthesis of (+)- and (-)-trypargine (6 steps and 38% overall yield), a 1-substituted β-carboline guanidine alkaloid isolated from the skin of the African frog K. senegalensis, was developed based on the construction of the b-carboline moiety via Bischler-Napieralski reaction and the enantioselective reduction of the dihydro-β-carboline intermediate via an asymmetric transfer hydrogenation reaction using Noyori's protocol. (author)

Control of electron localization to isolate and enhance molecular harmonic plateau in asymmetric HeH2+ system

International Nuclear Information System (INIS)

Lu, Ruifeng; Yu, Chao; Wang, Yunhui; Shi, Qi; Zhang, Yadong

2014-01-01

High-order harmonic generation from the asymmetric molecular ion HeH 2+ exposed to intense laser fields was investigated by quantum wave packet calculations in which the initial wave packet of HeH 2+ was prepared in the first excited 2pσ state. The calculated molecular harmonic plateau at low frequencies was effectively isolated and enhanced by adjusting the carrier-envelope phase (CEP) of the laser field. Furthermore, double-well model, time-dependent electronic density, electronic state population, and time-frequency analyses were presented to explain the underlying mechanism of the efficient isolated molecular plateau. By taking advantage of the CEP effect to control the electronic dynamics, this isolated molecular plateau can be used to generate high-intensity single attosecond pulses.

Stable walking with asymmetric legs

International Nuclear Information System (INIS)

Merker, Andreas; Rummel, Juergen; Seyfarth, Andre

2011-01-01

Asymmetric leg function is often an undesired side-effect in artificial legged systems and may reflect functional deficits or variations in the mechanical construction. It can also be found in legged locomotion in humans and animals such as after an accident or in specific gait patterns. So far, it is not clear to what extent differences in the leg function of contralateral limbs can be tolerated during walking or running. Here, we address this issue using a bipedal spring-mass model for simulating walking with compliant legs. With the help of the model, we show that considerable differences between contralateral legs can be tolerated and may even provide advantages to the robustness of the system dynamics. A better understanding of the mechanisms and potential benefits of asymmetric leg operation may help to guide the development of artificial limbs or the design novel therapeutic concepts and rehabilitation strategies.

Polarization dependent switching of asymmetric nanorings with a circular field

Directory of Open Access Journals (Sweden)

Nihar R. Pradhan

2016-01-01

Full Text Available We experimentally investigated the switching from onion to vortex states in asymmetric cobalt nanorings by an applied circular field. An in-plane field is applied along the symmetric or asymmetric axis of the ring to establish domain walls (DWs with symmetric or asymmetric polarization. A circular field is then applied to switch from the onion state to the vortex state, moving the DWs in the process. The asymmetry of the ring leads to different switching fields depending on the location of the DWs and direction of applied field. For polarization along the asymmetric axis, the field required to move the DWs to the narrow side of the ring is smaller than the field required to move the DWs to the larger side of the ring. For polarization along the symmetric axis, establishing one DW in the narrow side and one on the wide side, the field required to switch to the vortex state is an intermediate value.

[Combined orthodontic-orthoganthic surgery to treat asymmetric mandibular excess malocclusions].

Science.gov (United States)

Li, Xiao-Bing; Chen, Song; Chen, Yang-Xi; Li, Jun

2005-06-01

To discuss the skeletal and dentoalveolar characteristics of asymmetric mandibular excess malocclusions and to discuss the procedures of combined orthodontic-orthonganthic surgery treatments of asymmetric mandibular excess malocclusions. 25 cases treated by combined orthodontic-orthognathic surgery treatments were reviewed to find out the specialties of this kind of therapy. The asymmetric of mandible presents anterior and posterior teeth tipped both sagitally and horizontally, as well as upper and lower jaws incompatibility. The pre-surgical orthodontic treatments included decomposition of anterior and posterior teeth, leveling and aligning the teeth etc. The post-surgical orthodontic treatments were to detail the occlusions. The patients all got functional and aesthetic good results after the combined orthodontic-orthognathic surgery treatments. The asymmetric mandibular excess affects the harmony of the face badly, and the correction of it must be carried out by the combined orthodontic-orthognathic surgery treatments. The pre- and post-surgical orthodontic treatments are the key stages to make the skeletal corrections stable.

High Current Ionic Diode Using Homogeneously Charged Asymmetric Nanochannel Network Membrane.

Science.gov (United States)

Choi, Eunpyo; Wang, Cong; Chang, Gyu Tae; Park, Jungyul

2016-04-13

A high current ionic diode is achieved using an asymmetric nanochannel network membrane (NCNM) constructed by soft lithography and in situ self-assembly of nanoparticles with uniform surface charge. The asymmetric NCNM exhibits high rectified currents without losing a rectification ratio because of its ionic selectivity gradient and differentiated electrical conductance. Asymmetric ionic transport is analyzed with diode-like I-V curves and visualized via fluorescent dyes, which is closely correlated with ionic selectivity and ion distribution according to variation of NCNM geometries.

Design of activated carbon/activated carbon asymmetric capacitors

Science.gov (United States)

Piñeiro-Prado, Isabel; Salinas-Torres, David; Ruiz Rosas, Ramiro; Morallon, Emilia; Cazorla-Amoros, Diego

2016-03-01

Supercapacitors are energy storage devices that offer a high power density and a low energy density in comparison with batteries. Their limited energy density can be overcome by using asymmetric configuration in mass electrodes, where each electrode works within their maximum available potential window, rendering the maximum voltage output of the system. Such asymmetric capacitors must be optimized through careful electrochemical characterization of the electrodes for accurate determination of the capacitance and the potential stability limits. The results of the characterization are then used for optimizing mass ratio of the electrodes from the balance of stored charge. The reliability of the design largely depends on the approach taken for the electrochemical characterization. Therefore, the performance could be lower than expected and even the system could break down, if a well thought out procedure is not followed. In this work, a procedure for the development of asymmetric supercapacitors based on activated carbons is detailed. Three activated carbon materials with different textural properties and surface chemistry have been systematically characterized in neutral aqueous electrolyte. The asymmetric configuration of the masses of both electrodes in the supercapacitor has allowed to cover a higher potential window, resulting in an increase of the energy density of the three devices studied when compared with the symmetric systems, and an improved cycle life.

Design of activated carbon/activated carbon asymmetric capacitors

Directory of Open Access Journals (Sweden)

Isabel ePiñeiro-Prado

2016-03-01

Full Text Available Supercapacitors are energy storage devices that offer a high power density and a low energy density in comparison with batteries. Their limited energy density can be overcome by using asymmetric configuration in mass electrodes, where each electrode works within their maximum available potential window, rendering the maximum voltage output of the system. Such asymmetric capacitors must be optimized through careful electrochemical characterization of the electrodes for accurate determination of the capacitance and the potential stability limits. The results of the characterization are then used for optimizing mass ratio of the electrodes from the balance of stored charge. The reliability of the design largely depends on the approach taken for the electrochemical characterization. Therefore, the performance could be lower than expected and even the system could break down, if a well thought out procedure is not followed.In this work, a procedure for the development of asymmetric supercapacitors based on activated carbons is detailed. Three activated carbon materials with different textural properties and surface chemistry have been systematically characterized in neutral aqueous electrolyte. The asymmetric configuration of the masses of both electrodes in the supercapacitor has allowed to cover a higher potential window, resulting in an increase of the energy density of the three devices studied when compared with the symmetric systems, and an improved cycle life.

Direct catalytic asymmetric aldol-Tishchenko reaction.

Science.gov (United States)

Gnanadesikan, Vijay; Horiuchi, Yoshihiro; Ohshima, Takashi; Shibasaki, Masakatsu

2004-06-30

A direct catalytic asymmetric aldol reaction of propionate equivalent was achieved via the aldol-Tishchenko reaction. Coupling an irreversible Tishchenko reaction to a reversible aldol reaction overcame the retro-aldol reaction problem and thereby afforded the products in high enantio and diastereoselectivity using 10 mol % of the asymmetric catalyst. A variety of ketones and aldehydes, including propyl and butyl ketones, were coupled efficiently, yielding the corresponding aldol-Tishchenko products in up to 96% yield and 95% ee. Diastereoselectivity was generally below the detection limit of 1H NMR (>98:2). Preliminary studies performed to clarify the mechanism revealed that the aldol products were racemic with no diastereoselectivity. On the other hand, the Tishchenko products were obtained in a highly enantiocontrolled manner.

Ion Motion Stability in Asymmetric Surface Electrode Ion Traps

Science.gov (United States)

Shaikh, Fayaz; Ozakin, Arkadas

2010-03-01

Many recently developed designs of the surface electrode ion traps for quantum information processing have asymmetry built into their geometries. The asymmetry helps rotate the trap axes to angles with respect to electrode surface that facilitate laser cooling of ions but introduces a relative angle between the RF and DC fields and invalidates the classical stability analysis of the symmetric case for which the equations of motion are decoupled. For asymmetric case the classical motion of a single ion is given by a coupled, multi-dimensional version of Mathieu's equation. In this poster we discuss the stability diagram of asymmetric surface traps by performing an approximate multiple scale perturbation analysis of the coupled Mathieu equations, and validate the results with numerical simulations. After obtaining the stability diagram for the linear fields, we simulate the motion of an ion in a given asymmetric surface trap, utilizing a method-of-moments calculation of the electrode fields. We obtain the stability diagram and compare it with the ideal case to find the region of validity. Finally, we compare the results of our stability analysis to experiments conducted on a microfabricated asymmetric surface trap.

Asymmetric information and list-price reductions in the housing market

NARCIS (Netherlands)

de Wit, E.; van der Klaauw, B.

2013-01-01

In housing markets with asymmetric information list prices may signal unobserved properties of the house or the seller. Asymmetric information is the starting point for many models for the housing market. In this paper, we estimate the causal effect of list-price reductions on the time houses remain

JET and COMPASS asymmetrical disruptions

Czech Academy of Sciences Publication Activity Database

Gerasimov, S.N.; Abreu, P.; Baruzzo, M.; Drozdov, V.; Dvornova, A.; Havlíček, Josef; Hender, T.C.; Hronová-Bilyková, Olena; Kruezi, U.; Li, X.; Markovič, Tomáš; Pánek, Radomír; Rubinacci, G.; Tsalas, M.; Ventre, S.; Villone, F.; Zakharov, L.E.

2015-01-01

Roč. 55, č. 11 (2015), s. 113006-113006 ISSN 0029-5515 R&D Projects: GA MŠk(CZ) LM2011021 Institutional support: RVO:61389021 Keywords : tokamak * asymmetrical disruption * JET * COMPASS Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 4.040, year: 2015

Magnetically Modified Asymmetric Supercapacitors, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — This Small Business Innovation Research Phase I project is for the development of an asymmetric supercapacitor that will have improved energy density and cycle life....

Positioning the 5'-flap junction in the active site controls the rate of flap endonuclease-1-catalyzed DNA cleavage

KAUST Repository

Song, Bo

2018-02-09

Flap endonucleases catalyze cleavage of single-stranded DNA flaps formed during replication, repair and recombination, and are therefore essential for genome processing and stability. Recent crystal structures of DNA-bound human flap endonuclease (hFEN1) offer new insights into how conformational changes in the DNA and hFEN1 may facilitate the reaction mechanism. For example, previous biochemical studies of DNA conformation performed under non-catalytic conditions with Ca2+ have suggested that base unpairing at the 5\\'-flap:template junction is an important step in the reaction, but the new structural data suggest otherwise. To clarify the role of DNA changes in the kinetic mechanism, we measured a series of transient steps - from substrate binding to product release - during the hFEN1-catalyzed reaction in the presence of Mg2+. We found that while hFEN1 binds and bends DNA at a fast, diffusion-limited rate, much slower Mg2+-dependent conformational changes in DNA around the active site are subsequently necessary and rate-limiting for 5\\'-flap cleavage. These changes are reported overall by fluorescence of 2-aminopurine at the 5\\'-flap:template junction, indicating that local DNA distortion (e.g., disruption of base stacking observed in structures), associated with positioning the 5\\'-flap scissile phosphodiester bond in the hFEN1 active site, controls catalysis. hFEN1 residues with distinct roles in the catalytic mechanism, including those binding metal ions (Asp-34, Asp-181), steering the 5\\'-flap through the active site and binding the scissile phosphate (Lys-93, Arg-100), and stacking against the base 5\\' to the scissile phosphate (Tyr-40), all contribute to these rate-limiting conformational changes, ensuring efficient and specific cleavage of 5\\'-flaps.

Haplotype-based case-control study on human apurinic/apyrimidinic endonuclease 1/redox effector factor-1 gene and essential hypertension.

Science.gov (United States)

Naganuma, Takahiro; Nakayama, Tomohiro; Sato, Naoyuki; Fu, Zhenyan; Soma, Masayoshi; Yamaguchi, Mai; Shimodaira, Masanori; Aoi, Noriko; Usami, Ron

2010-02-01

Oxidative DNA damage is involved in the pathophysiology of essential hypertension (EH), which is a multifactorial disorder. Apurinic/apyrimidinic endonuclease 1/redox effector factor-1 (APE1/REF-1) is an essential endonuclease in the base excision repair pathway of oxidatively damaged DNA, in addition to having reducing properties that promote the binding of redox-sensitive transcription factors. Blood pressure in APE1/REF-1-knockout mice is reported to be significantly higher than in wild-type mice. The aim of this study was to investigate the relationship between EH and the human APE1/REF-1 gene through a haplotype-based case-control study using single-nucleotide polymorphisms (SNPs). We selected five SNPs in the human APE1/REF-1 gene (rs1760944, rs3136814, rs17111967, rs3136817, and rs1130409), and performed case-control studies in 265 EH patients and 266 age-matched normotensive (NT) subjects. rs17111967 was found to show nonheterogeneity among Japanese subjects. There were no significant differences in the overall distribution of genotypes or alleles for each SNP between EH and NT groups. In the overall distribution of the haplotype-based case-control study constructed based on rs1760944, rs3136817, and rs1130409, the frequency of the G-T-T haplotype was significantly higher in the EH group than in the NT group (2.1% vs. 0.0%, P = 0.001). Multiple logistic regression analysis also revealed significant differences for the G-T-T haplotype, even after adjustment for confounding factors (OR = 8.600, 95% CI: 1.073-68.951, P = 0.043). Based on the present results, the G-T-T haplotype appears to be a genetic marker of EH, and the APE1/REF-1 gene appears to be a susceptibility gene for EH.

Positioning the 5'-flap junction in the active site controls the rate of flap endonuclease-1-catalyzed DNA cleavage

KAUST Repository

Song, Bo; Hamdan, Samir; Hingorani, Manju M

2018-01-01

Flap endonucleases catalyze cleavage of single-stranded DNA flaps formed during replication, repair and recombination, and are therefore essential for genome processing and stability. Recent crystal structures of DNA-bound human flap endonuclease (hFEN1) offer new insights into how conformational changes in the DNA and hFEN1 may facilitate the reaction mechanism. For example, previous biochemical studies of DNA conformation performed under non-catalytic conditions with Ca2+ have suggested that base unpairing at the 5'-flap:template junction is an important step in the reaction, but the new structural data suggest otherwise. To clarify the role of DNA changes in the kinetic mechanism, we measured a series of transient steps - from substrate binding to product release - during the hFEN1-catalyzed reaction in the presence of Mg2+. We found that while hFEN1 binds and bends DNA at a fast, diffusion-limited rate, much slower Mg2+-dependent conformational changes in DNA around the active site are subsequently necessary and rate-limiting for 5'-flap cleavage. These changes are reported overall by fluorescence of 2-aminopurine at the 5'-flap:template junction, indicating that local DNA distortion (e.g., disruption of base stacking observed in structures), associated with positioning the 5'-flap scissile phosphodiester bond in the hFEN1 active site, controls catalysis. hFEN1 residues with distinct roles in the catalytic mechanism, including those binding metal ions (Asp-34, Asp-181), steering the 5'-flap through the active site and binding the scissile phosphate (Lys-93, Arg-100), and stacking against the base 5' to the scissile phosphate (Tyr-40), all contribute to these rate-limiting conformational changes, ensuring efficient and specific cleavage of 5'-flaps.

Ideal MHD beta-limits of poloidally asymmetric equilibria

Energy Technology Data Exchange (ETDEWEB)

Todd, A.M.M.; Miller, A.E.; Grimm, R.C.; Okabayashi, M.; Dalhed, H.E. Jr.

1981-05-01

The ideal MHD stability of poloidally asymmetric equilibria, which are typical of a tokamak reactor design with a single-null poloidal divertor is examined. As with symmetric equilibria, stability to non-axisymmetric modes improves with increasing triangularity and ellipticity, and with lower edge safety factor. Pressure profiles optimized with respect to ballooning stability are obtained for an asymmetric shape, resulting in ..beta../sub critical/ approx. = 5.7%. The corresponding value for an equivalent symmetric shape is ..beta../sub critical/ approx. = 6.5%.

Ideal MHD beta-limits of poloidally asymmetric equilibria

International Nuclear Information System (INIS)

Todd, A.M.M.; Miller, A.E.; Grimm, R.C.; Okabayashi, M.; Dalhed, H.E. Jr.

1981-05-01

The ideal MHD stability of poloidally asymmetric equilibria, which are typical of a tokamak reactor design with a single-null poloidal divertor is examined. As with symmetric equilibria, stability to non-axisymmetric modes improves with increasing triangularity and ellipticity, and with lower edge safety factor. Pressure profiles optimized with respect to ballooning stability are obtained for an asymmetric shape, resulting in β/sub critical/ approx. = 5.7%. The corresponding value for an equivalent symmetric shape is β/sub critical/ approx. = 6.5%

Six transformer based asymmetrical embedded Z-source inverters

DEFF Research Database (Denmark)

Wei, Mo; Poh Chiang, Loh; Chi, Jin

2013-01-01

Embedded/Asymmetrical embedded Z-source inverters were proposed to maintain smooth input current/voltage across the dc source and within the impedance network, remain the shoot-through feature used to boost up the dc-link voltage without adding bulky filter at input side. This paper introduces a ...... a class of transformer based asymmetrical embedded Z-source inverters which keep the smooth input current and voltage while achieving enhanced voltage boost capability. The presented inverters are verified by laboratory prototypes experimentally....

Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1

KAUST Repository

Sobhy, M.; Joudeh, L.; Huang, X.; Takahashi, Masateru; Hamdan, S.

2013-01-01

Human flap endonuclease 1 (FEN1), one of the structure-specific 5' nucleases, is integral in replication, repair, and recombination of cellular DNA. The 5' nucleases share significant unifying features yet cleave diverse substrates at similar positions relative to 5' end junctions. Using single-molecule Förster resonance energy transfer, we find a multistep mechanism that verifies all substrate features before inducing the intermediary-DNA bending step that is believed to unify 5' nuclease mechanisms. This is achieved by coordinating threading of the 5' flap of a nick junction into the conserved capped-helical gateway, overseeing the active site, and bending by binding at the base of the junction. We propose that this sequential and multistep substrate recognition process allows different 5' nucleases to recognize different substrates and restrict the induction of DNA bending to the last common step. Such mechanisms would also ensure the protection ofDNA junctions from nonspecific bending and cleavage. 2013 The Authors.

Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1

KAUST Repository

Sobhy, M.

2013-06-06

Human flap endonuclease 1 (FEN1), one of the structure-specific 5\\' nucleases, is integral in replication, repair, and recombination of cellular DNA. The 5\\' nucleases share significant unifying features yet cleave diverse substrates at similar positions relative to 5\\' end junctions. Using single-molecule Förster resonance energy transfer, we find a multistep mechanism that verifies all substrate features before inducing the intermediary-DNA bending step that is believed to unify 5\\' nuclease mechanisms. This is achieved by coordinating threading of the 5\\' flap of a nick junction into the conserved capped-helical gateway, overseeing the active site, and bending by binding at the base of the junction. We propose that this sequential and multistep substrate recognition process allows different 5\\' nucleases to recognize different substrates and restrict the induction of DNA bending to the last common step. Such mechanisms would also ensure the protection ofDNA junctions from nonspecific bending and cleavage. 2013 The Authors.

Synchronised and complementary coordination mechanisms in an asymmetric joint aiming task

DEFF Research Database (Denmark)

Skewes, Joshua Charles; Skewes, Lea; Michael, John

2015-01-01

Many forms of social interaction require that behaviour be coordinated in the here and now. Much research has been conducted on how people coordinate their actions in real time to achieve a joint goal, showing that people use both synchronised (i.e. symmetric) and complementary (i.e. asymmetric) ...... in this asymmetric task, as people synchronise better with an irregular, but adaptive partner, than with a completely predictable, but non-responsive metronome. These results show that given asymmetric task constraints, adaptability, rather than predictability facilitates coordination....

Capability of DFIG WTS to ride through recurring asymmetrical grid faults

DEFF Research Database (Denmark)

Chen, Wenjie; Blaabjerg, Frede; Chen, Min

2014-01-01

The Wind Turbine Systems (WTS) are required to ride through recurring grid faults in some countries. In this paper, the capability of Doubly Fed Induction Generator (DFIG) WTS to ride through recurring asymmetrical grid faults is evaluated and compared with the ride through capability under single...... asymmetrical grid fault. A mathematical model of the DFIG under recurring asymmetrical grid faults is represented. The analysis are verified by simulations on a 1.5MW DFIG model and by experiments on a reduced-scale DFIG test system....

Effect of the magnetic field on the nonlinear optical rectification and second and third harmonic generation in double δ-doped GaAs quantum wells

Science.gov (United States)

Martínez-Orozco, J. C.; Rojas-Briseño, J. G.; Rodríguez-Magdaleno, K. A.; Rodríguez-Vargas, I.; Mora-Ramos, M. E.; Restrepo, R. L.; Ungan, F.; Kasapoglu, E.; Duque, C. A.

2017-11-01

In this paper we are reporting the computation for the Nonlinear Optical Rectification (NOR) and the Second and Third Harmonic Generation (SHG and THG) related with electronic states of asymmetric double Si-δ-doped quantum well in a GaAs matrix when this is subjected to an in-plane (x-oriented) constant magnetic field effect. The work is performed in the effective mass and parabolic band approximations in order to compute the electronic structure for the system by a diagonalization procedure. The expressions for the nonlinear optical susceptibilities, χ0(2), χ2ω(2), and χ3ω(3), are those arising from the compact matrix density formulation and stand for the NOR, SHG, and THG, respectively. This asymmetric double δ-doped quantum well potential profile actually exhibits nonzero NOR, SHG, and THG responses which can be easily controlled by the in-plane (x-direction) externally applied magnetic field. In particular we find that for the chosen configuration the harmonic generation is in the far-infrared/THz region, thus and becoming suitable building blocks for photodetectors in this range of the electromagnetic spectra.

Influence of artificial tip perturbation on asymmetric vortices flow over a chined fuselage

Directory of Open Access Journals (Sweden)

Shi Wei

2015-08-01

Full Text Available An experimental study was conducted with the aim of understanding behavior of asymmetric vortices flow over a chined fuselage. The tests were carried out in a wind tunnel at Reynolds number of 1.87 × 105 under the conditions of high angles of attack and zero angle of sideslip. The results show that leeward vortices flow becomes asymmetric vortices flow when angle of attack increases over 20°. The asymmetric vortices flow is asymmetry of two forebody vortices owing to the increase of angle of attack but not asymmetry of vortex breakdown which appears when angle of attack is above 35°. Asymmetric vortices flow is sensitive to tip perturbation and is non-deterministic due to randomly distributed natural minute geometrical irregularities on the nose tip within machining tolerance. Deterministic asymmetric vortices flow can be obtained by attaching artificial tip perturbation which can trigger asymmetric vortices flow and decide asymmetric vortices flow pattern. Triggered by artificial tip perturbation, the vortex on the same side with perturbation is in a higher position, and the other vortex on the opposite side is in a lower position. Vortex suction on the lower vortex side is larger, which corresponds to a side force pointing to the lower vortex side.

Perturbation solutions for flow through symmetrical hoppers with inserts and asymmetrical wedge hoppers

Science.gov (United States)

Cox, G. M.; Mccue, S. W.; Thamwattana, N.; Hill, J. M.

Under certain circumstances, an industrial hopper which operates under the "funnel-flow" regime can be converted to the "mass-flow" regime with the addition of a flow-corrective insert. This paper is concerned with calculating granular flow patterns near the outlet of hoppers that incorporate a particular type of insert, the cone-in-cone insert. The flow is considered to be quasi-static, and governed by the Coulomb-Mohr yield condition together with the non-dilatant double-shearing theory. In two-dimensions, the hoppers are wedge-shaped, and as such the formulation for the wedge-in-wedge hopper also includes the case of asymmetrical hoppers. A perturbation approach, valid for high angles of internal friction, is used for both two-dimensional and axially symmetric flows, with analytic results possible for both leading order and correction terms. This perturbation scheme is compared with numerical solutions to the governing equations, and is shown to work very well for angles of internal friction in excess of 45°.

Host Factors Influencing the Retrohoming Pathway of Group II Intron RmInt1, Which Has an Intron-Encoded Protein Naturally Devoid of Endonuclease Activity.

Directory of Open Access Journals (Sweden)

Rafael Nisa-Martínez

Full Text Available Bacterial group II introns are self-splicing catalytic RNAs and mobile retroelements that have an open reading frame encoding an intron-encoded protein (IEP with reverse transcriptase (RT and RNA splicing or maturase activity. Some IEPs carry a DNA endonuclease (En domain, which is required to cleave the bottom strand downstream from the intron-insertion site for target DNA-primed reverse transcription (TPRT of the inserted intron RNA. Host factors complete the insertion of the intron. By contrast, the major retrohoming pathway of introns with IEPs naturally lacking endonuclease activity, like the Sinorhizobium meliloti intron RmInt1, is thought to involve insertion of the intron RNA into the template for lagging strand DNA synthesis ahead of the replication fork, with possible use of the nascent strand to prime reverse transcription of the intron RNA. The host factors influencing the retrohoming pathway of such introns have not yet been described. Here, we identify key candidates likely to be involved in early and late steps of RmInt1 retrohoming. Some of these host factors are common to En+ group II intron retrohoming, but some have different functions. Our results also suggest that the retrohoming process of RmInt1 may be less dependent on the intracellular free Mg2+ concentration than those of other group II introns.

Autorefraction versus subjective refraction in a radially asymmetric multifocal intraocular lens

NARCIS (Netherlands)

Linden, J.W.M. van der; Vrijman, V.; El-Saady, R.; Meulen, I.J. van der; Mourits, M.P.; Lapid-Gortzak, R.

2014-01-01

PURPOSE: To evaluate whether the automated refraction (AR) correlates with subjective manifest (MR) refraction in eyes implanted with radially asymmetric multifocal intraocular lens (IOLs). METHODS: This retrospective study evaluated 52 eyes (52 patients) implanted with a radially asymmetric

Electron Jet of Asymmetric Reconnection

Science.gov (United States)

Khotyaintsev, Yu. V.; Graham, D. B.; Norgren, C.; Eriksson, E.; Li, W.; Johlander, A.; Vaivads, A.; Andre, M.; Pritchett, P. L.; Retino, A.;

Field factors for asymmetric collimators

International Nuclear Information System (INIS)

Turner, J.R.; Butler, A.P.H.

1996-01-01

In recent years manufacturers have been supplying linear accelerators with either a single pair or a dual pair of collimators. The use of a model to relate off-axis field factors to on-axis field factors obviates the need for repeat measurements whenever the asymmetric collimators are employed. We have investigated the variation of collimator scatter Sc, with distance of the central ray x from the central axis for a variety of non square field sizes. Collimator scatter was measured by in-air measurements with a build-up cap. The Primaty-Off-Centre-Ratio (POCR) was measured in-air by scanning orthogonally across the beam with an ionization chamber. The result of the investigation is the useful prediction of off-axis field factors for a range of rectangular asymmetric fields using the simple product of the on-axis field factor and the POCR in air. The effect of asymmetry on the quality of the beam and hence the percent depth dose will be discussed. (author)

The effects of asymmetric directional microphone fittings on acceptance of background noise.

Science.gov (United States)

Kim, Jong S; Bryan, Melinda Freyaldenhoven

2011-05-01

The effects of asymmetric directional microphone fittings (i.e., an omnidirectional microphone on one ear and a directional microphone on the other) on speech understanding in noise and acceptance of background noise were investigated in 15 full-time hearing aid users. Subjects were fitted binaurally with four directional microphone conditions (i.e., binaural omnidirectional, right asymmetric directional, left asymmetric directional and binaural directional microphones) using Siemens Intuis Directional behind-the-ear hearing aids. Speech understanding in noise was assessed using the Hearing in Noise Test, and acceptance of background noise was assessed using the Acceptable Noise Level procedure. Speech was presented from 0° while noise was presented from 180° azimuth. The results revealed that speech understanding in noise improved when using asymmetric directional microphones compared to binaural omnidirectional microphone fittings and was not significantly hindered compared to binaural directional microphone fittings. The results also revealed that listeners accepted more background noise when fitted with asymmetric directional microphones as compared to binaural omnidirectional microphones. Lastly, the results revealed that the acceptance of noise was further increased for the binaural directional microphones when compared to the asymmetric directional microphones, maximizing listeners' willingness to accept background noise in the presence of noise. Clinical implications will be discussed.

Plasma polymerization at different positions in an asymmetric ethylene discharge

International Nuclear Information System (INIS)

Trieschmann, Jan; Hegemann, Dirk

2011-01-01

The characteristics of plasma polymerization are investigated in an asymmetric, capacitively coupled plasma discharge. Here, the deposition in different plasma zones, i.e. on the driven electrode, within the plasma bulk and the plasma sheath as well as approximately at the plasma-sheath edge, is investigated. Principal expectations are perfectly met, though new interesting dependences of the obtained a-C : H coatings with respect to film properties and deposition rates are also found. That is, the deposition rates as measured on thin, small glass slides placed directly on the electrode are considerably higher than everywhere else in the plasma, yet only single-sided. In contrast, the deposition rates on the samples within the plasma are lowered depending on the exact placement, while a double-sided coating is obtained. Furthermore, film properties, such as the film density, are highly dependent on the sample placement in the plasma, which can even be higher under floating conditions. With simple physical arguments we are able to show the relations between the deposition rate and the energy input into the plasma as well as between the energy density during film growth and the film density itself.

Beam-beam issues in asymmetric colliders

International Nuclear Information System (INIS)

Furman, M.A.

1992-07-01

We discuss generic beam-beam issues for proposed asymmetric e + - e - colliders. We illustrate the issues by choosing, as examples, the proposals by Cornell University (CESR-B), KEK, and SLAC/LBL/LLNL (PEP-II)

Autorefraction versus subjective refraction in a radially asymmetric multifocal intraocular lens

NARCIS (Netherlands)

van der Linden, Jan Willem; Vrijman, Violette; Al-Saady, Rana; El-Saady, Rana; van der Meulen, Ivanka J.; Mourits, Maarten P.; Lapid-Gortzak, Ruth

2014-01-01

To evaluate whether the automated refraction (AR) correlates with subjective manifest (MR) refraction in eyes implanted with radially asymmetric multifocal intraocular lens (IOLs). This retrospective study evaluated 52 eyes (52 patients) implanted with a radially asymmetric multifocal IOL (LS-312

A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation.

Science.gov (United States)

Ponder, Rebecca G; Fonville, Natalie C; Rosenberg, Susan M

2005-09-16

Special mechanisms of mutation are induced in microbes under growth-limiting stress causing genetic instability, including occasional adaptive mutations that may speed evolution. Both the mutation mechanisms and their control by stress have remained elusive. We provide evidence that the molecular basis for stress-induced mutagenesis in an E. coli model is error-prone DNA double-strand break repair (DSBR). I-SceI-endonuclease-induced DSBs strongly activate stress-induced mutations near the DSB, but not globally. The same proteins are required as for cells without induced DSBs: DSBR proteins, DinB-error-prone polymerase, and the RpoS starvation-stress-response regulator. Mutation is promoted by homology between cut and uncut DNA molecules, supporting a homology-mediated DSBR mechanism. DSBs also promote gene amplification. Finally, DSBs activate mutation only during stationary phase/starvation but will during exponential growth if RpoS is expressed. Our findings reveal an RpoS-controlled switch from high-fidelity to mutagenic DSBR under stress. This limits genetic instability both in time and to localized genome regions, potentially important evolutionary strategies.

The asymmetric rotator model applied to odd-mass iridium isotopes

International Nuclear Information System (INIS)

Piepenbring, R.

1980-04-01

The method of inversion of the eigenvalue problem previously developed for nuclei with axial symmetry is extended to asymmetric equilibrium shapes. This new approach of the asymmetric rotator model is applied to the odd-mass iridium isotopes. A satisfactory and coherent description of the observed energy spectra is obtained, especially for the lighter isotopes

All Pseudocapacitive MXene-RuO2 Asymmetric Supercapacitors

KAUST Repository

Jiang, Qiu

2018-01-23

2D transition metal carbides and nitrides, known as MXenes, are an emerging class of 2D materials with a wide spectrum of potential applications, in particular in electrochemical energy storage. The hydrophilicity of MXenes combined with their metallic conductivity and surface redox reactions is the key for high-rate pseudocapacitive energy storage in MXene electrodes. However, symmetric MXene supercapacitors have a limited voltage window of around 0.6 V due to possible oxidation at high anodic potentials. In this study, the fact that titanium carbide MXene (Ti3C2Tx) can operate at negative potentials in acidic electrolyte is exploited, to design an all-pseudocapacitive asymmetric device by combining it with a ruthenium oxide (RuO2) positive electrode. This asymmetric device operates at a voltage window of 1.5 V, which is about two times wider than the operating voltage window of symmetric MXene supercapacitors, and is the widest voltage window reported to date for MXene-based supercapacitors. The complementary working potential windows of MXene and RuO2, along with proton-induced pseudocapacitance, significantly enhance the device performance. As a result, the asymmetric devices can deliver an energy density of 37 µW h cm−2 at a power density of 40 mW cm−2, with 86% capacitance retention after 20 000 charge–discharge cycles. These results show that pseudocapacitive negative MXene electrodes can potentially replace carbon-based materials in asymmetric electrochemical capacitors, leading to an increased energy density.

DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway

NARCIS (Netherlands)

van den Broek, B.; Noom, M.C.; Wuite, G.J.L.

2005-01-01

Type II restriction endonucleases protect bacteria against phage infections by cleaving recognition sites on foreign double-stranded DNA (dsDNA) with extraordinary specificity. This capability arises primarily from large conformational changes in enzyme and/or DNA upon target sequence recognition.

Asymmetric Facial Bone Fragmentation Mirrors Asymmetric Distribution of Cranial Neuromasts in Blind Mexican Cavefish

Directory of Open Access Journals (Sweden)

Joshua B. Gross

2016-10-01

Full Text Available Craniofacial asymmetry is a convergent trait widely distributed across animals that colonize the extreme cave environment. Although craniofacial asymmetry can be discerned easily, other complex phenotypes (such as sensory organ position and numerical variation are challenging to score and compare. Certain bones of the craniofacial complex demonstrate substantial asymmetry, and co-localize to regions harboring dramatically expanded numbers of mechanosensory neuromasts. To determine if a relationship exists between this expansion and bone fragmentation in cavefish, we developed a quantitative measure of positional symmetry across the left-right axis. We found that three different cave-dwelling populations were significantly more asymmetric compared to surface-dwelling fish. Moreover, cave populations did not differ in the degree of neuromast asymmetry. This work establishes a method for quantifying symmetry of a complex phenotype, and demonstrates that facial bone fragmentation mirrors the asymmetric distribution of neuromasts in different cavefish populations. Further developmental studies will provide a clearer picture of the developmental and cellular changes that accompany this extreme phenotype, and help illuminate the genetic basis for facial asymmetry in vertebrates.

Impact of asymmetric lamp positioning on the performance of a closed-conduit UV reactor

Directory of Open Access Journals (Sweden)

Tipu Sultan

2017-06-01

Full Text Available Computational fluid dynamics (CFD analyses for the performance improvement of a closed-conduit ultraviolet (UV reactor were performed by changing the lamp positions from symmetric to asymmetric. The asymmetric lamp positioning can be useful for UV reactor design and optimization. This goal was achieved by incorporating the two performance factors, namely reduction equivalent dose (RED and system dose performance. Four cases were carried out for asymmetric lamp positioning within the UV reactor chamber and each case consisted of four UV lamps that were simulated once symmetrically and four times asymmetrically. The results of the four asymmetric cases were compared with the symmetric one. Moreover, these results were evaluated by using CFD simulations of a closed-conduit UV reactor. The fluence rate model, UVCalc3D was employed to validate the simulations results. The simulation results provide detailed information about the dose distribution, pathogen track modeling and RED. The RED value was increased by approximately 15% by using UVCalc3D fluence rate model. Additionally, the asymmetric lamp positioning of the UV lamps had more than 50% of the pathogens received a better and a higher UV dose than in the symmetric case. Consequently, the system dose performance was improved by asymmetric lamp positioning. It was concluded that the performance parameters (higher RED and system dose performance were improved by using asymmetric lamp positioning.

Electron Raman scattering in asymmetrical multiple quantum wells

International Nuclear Information System (INIS)

Betancourt-Riera, R; Rosas, R; Marin-Enriquez, I; Riera, R; Marin, J L

2005-01-01

Optical properties of asymmetrical multiple quantum wells for the construction of quantum cascade lasers are calculated, and expressions for the electronic states of asymmetrical multiple quantum wells are presented. The gain and differential cross-section for an electron Raman scattering process are obtained. Also, the emission spectra for several scattering configurations are discussed, and the corresponding selection rules for the processes involved are studied; an interpretation of the singularities found in the spectra is given. The electron Raman scattering studied here can be used to provide direct information about the efficiency of the lasers

Preview-based Asymmetric Load Reduction of Wind Turbines

DEFF Research Database (Denmark)

Madsen, Mathias; Filsø, Jakob; Soltani, Mohsen

2012-01-01

Controller (MPC) developed is based on a model with individual blade pitching to utilize the LIDAR measurements. The MPC must also maintain a given power reference while satisfying a set of actuator constraints. The designed controller was tested on a 5 MW wind turbine in the FAST simulator and compared......Fatigue loads on wind turbines caused by an asymmetric wind field become an increasing concern when the scale of wind turbines increases. This paper presents a model based predictive approach to reduce asymmetric loads by using Light Detection And Ranging (LIDAR) measurements. The Model Predictive...

Single-electron tunneling in double-barrier nanostructures

International Nuclear Information System (INIS)

Goldman, V.J.; Su, B.; Cunningham, J.E.

1992-01-01

In this paper, the authors review experimental study of charge transport in nanometer double-barrier resonant tunneling devices. Heterostructure material is asymmetric: one barrier is substantially less transparent than the other. Resonant tunneling through size-quantized well states and single-electron charging of the well are thus largely separated in the two bias polarities. When the emitter barrier is more transparent than the collector barrier, electrons accumulate in the well; incremental electron occupation of the well is accompanied by Coulomb blockade leading to sharp steps of the tunneling current. When the emitter barrier is less transparent, the current reflects resonant tunneling of just one electron at a time through size-quantized well states; the current peaks and/or steps (depending on experimental parameters) appear in current-voltage characteristics. Magnetic field and temperature effects are also reviewed. Good agreement is achieved in comparison of many features of experimental data with simple theoretical models

Prospects of asymmetrically H-terminated zigzag germanene nanoribbons for spintronic application

Energy Technology Data Exchange (ETDEWEB)

Sharma, Varun, E-mail: varun@iiitm.ac.in [Nanomaterials Research Group, ABV-Indian Institute of Information Technology and Management (IIITM), Gwalior 474015 (India); Srivastava, Pankaj [Nanomaterials Research Group, ABV-Indian Institute of Information Technology and Management (IIITM), Gwalior 474015 (India); Jaiswal, Neeraj K. [Discipline of Physics, Indian Institute of Information Technology, Design & Manufacturing, Jabalpur, Dumna Airport Road, Jabalpur 482005 (India)

2017-02-28

Highlights: • Asymmetric hydrogen termination of Zigzag Germanene Nanoribbons (ZGeNR) is presented with their plausible spintronic device application. • It is revealed that asymmetric terminations are energetically more favourable compared to symmetric terminations. • The magnetic moment analysis depicts that asymmetric ZGeNR have a magnetic ground state with a preferred ferromagnetic (FM) coupling. • Presented doped asymmetric ZGeNR exhibits a half-metallic character which makes them qualify for spin-filtering device. - Abstract: First-principles investigations have been performed to explore the spin based electronic and transport properties of asymmetrically H-terminated zigzag germanene nanoribbons (2H−H ZGeNR). Investigations reveal a significant formation energy difference (ΔE{sub F} = E{sub F(2H-H)} − E{sub F(H-H)} ∼ −0.49 eV), highlighting more energetic stability for asymmetric edge termination compared to symmetric edge termination, irrespective of the ribbon width. Further, magnetic moment analysis and total energy calculations were performed to unveil that these structures have a magnetic ground state with preferred ferromagnetic (FM) coupling. The calculated E-k structures project a unique bipolar semiconducting behaviour for 2H−H ZGeNR which is contrast to H-terminated ZGeNR. Half-metallic transformation has also been revealed via suitable p-type or n-type doping for these structures. Finally, transport calculations were performed to highlight the selective contributions of spin-down (spin-up) electrons in the I–V characteristics of the doped 2H−H ZGeNR, suggesting their vitality for spintronic device applications.

The Respiratory Impedance in an Asymmetric Model of the Lung Structure

Directory of Open Access Journals (Sweden)

Robin De Keyser

2011-01-01

Full Text Available This paper presents a model of the respiratory tree as a recurrent, but asymmetric, structure. The intrinsic properties posed by such a system lead to a multi-fractal structure, i.e. a non-integer order model of the total impedance. The fractional order behavior of the asymmetric tree simulated as a dynamic system is assessed by means of Bode plots, on a wide range of frequencies. The results indicate than in a specific frequency range, both the symmetric
and asymmetric representation of the respiratory tree lead to similar values in the impedance.

Process for fabricating PBI hollow fiber asymmetric membranes for gas separation and liquid separation

Science.gov (United States)

Jayaweera, Indira; Krishnan, Gopala N.; Sanjurjo, Angel; Jayaweera, Palitha; Bhamidi, Srinivas

2016-04-26

The invention provides methods for preparing an asymmetric hollow fiber, the asymmetric hollow fibers prepared by such methods, and uses of the asymmetric hollow fibers. One method involves passing a polymeric solution through an outer annular orifice of a tube-in-orifice spinneret, passing a bore fluid though an inner tube of the spinneret, dropping the polymeric solution and bore fluid through an atmosphere over a dropping distance, and quenching the polymeric solution and bore fluid in a bath to form an asymmetric hollow fiber.

Bianisotropic metamaterials based on twisted asymmetric crosses

International Nuclear Information System (INIS)

Reyes-Avendaño, J A; Sampedro, M P; Juárez-Ruiz, E; Pérez-Rodríguez, F

2014-01-01

The effective bianisotropic response of 3D periodic metal-dielectric structures, composed of crosses with asymmetrically-cut wires, is investigated within a general homogenization theory using the Fourier formalism and the form-factor division approach. It is found that the frequency dependence of the effective permittivity for a system of periodically-repeated layers of metal crosses exhibits two strong resonances, whose separation is due to the cross asymmetry. Besides, bianisotropic metamaterials, having a base of four twisted asymmetric crosses, are proposed. The designed metamaterials possess negative refractive index at frequencies determined by the cross asymmetry, the gap between the arms of adjacent crosses lying on the same plane, and the type of Bravais lattice. (papers)

Double coupling: modeling subjectivity and asymmetric organization in social-ecological systems

Directory of Open Access Journals (Sweden)

David Manuel-Navarrete

2015-09-01

Full Text Available Social-ecological organization is a multidimensional phenomenon that combines material and symbolic processes. However, the coupling between social and ecological subsystem is often conceptualized as purely material, thus reducing the symbolic dimension to its behavioral and actionable expressions. In this paper I conceptualize social-ecological systems as doubly coupled. On the one hand, material expressions of socio-cultural processes affect and are affected by ecological dynamics. On the other hand, coupled social-ecological material dynamics are concurrently coupled with subjective dynamics via coding, decoding, personal experience, and human agency. This second coupling operates across two organizationally heterogeneous dimensions: material and symbolic. Although resilience thinking builds on the recognition of organizational asymmetry between living and nonliving systems, it has overlooked the equivalent asymmetry between ecological and socio-cultural subsystems. Three guiding concepts are proposed to formalize double coupling. The first one, social-ecological asymmetry, expands on past seminal work on ecological self-organization to incorporate reflexivity and subjectivity in social-ecological modeling. Organizational asymmetry is based in the distinction between social rules, which are symbolically produced and changed through human agents' reflexivity and purpose, and biophysical rules, which are determined by functional relations between ecological components. The second guiding concept, conscious power, brings to the fore human agents' distinctive capacity to produce our own subjective identity and the consequences of this capacity for social-ecological organization. The third concept, congruence between subjective and objective dynamics, redefines sustainability as contingent on congruent relations between material and symbolic processes. Social-ecological theories and analyses based on these three guiding concepts would support the

Asymmetric Distribution of GFAP in Glioma Multipotent Cells

Science.gov (United States)

Guichet, Pierre-Olivier; Guelfi, Sophie; Ripoll, Chantal; Teigell, Marisa; Sabourin, Jean-Charles; Bauchet, Luc; Rigau, Valérie; Rothhut, Bernard; Hugnot, Jean-Philippe

2016-01-01

Asymmetric division (AD) is a fundamental mechanism whereby unequal inheritance of various cellular compounds during mitosis generates unequal fate in the two daughter cells. Unequal repartitions of transcription factors, receptors as well as mRNA have been abundantly described in AD. In contrast, the involvement of intermediate filaments in this process is still largely unknown. AD occurs in stem cells during development but was also recently observed in cancer stem cells. Here, we demonstrate the asymmetric distribution of the main astrocytic intermediate filament, namely the glial fibrillary acid protein (GFAP), in mitotic glioma multipotent cells isolated from glioblastoma (GBM), the most frequent type of brain tumor. Unequal mitotic repartition of GFAP was also observed in mice non-tumoral neural stem cells indicating that this process occurs across species and is not restricted to cancerous cells. Immunofluorescence and videomicroscopy were used to capture these rare and transient events. Considering the role of intermediate filaments in cytoplasm organization and cell signaling, we propose that asymmetric distribution of GFAP could possibly participate in the regulation of normal and cancerous neural stem cell fate. PMID:26953813

Asymmetric Distribution of GFAP in Glioma Multipotent Cells.

Directory of Open Access Journals (Sweden)

Pierre-Olivier Guichet

Full Text Available Asymmetric division (AD is a fundamental mechanism whereby unequal inheritance of various cellular compounds during mitosis generates unequal fate in the two daughter cells. Unequal repartitions of transcription factors, receptors as well as mRNA have been abundantly described in AD. In contrast, the involvement of intermediate filaments in this process is still largely unknown. AD occurs in stem cells during development but was also recently observed in cancer stem cells. Here, we demonstrate the asymmetric distribution of the main astrocytic intermediate filament, namely the glial fibrillary acid protein (GFAP, in mitotic glioma multipotent cells isolated from glioblastoma (GBM, the most frequent type of brain tumor. Unequal mitotic repartition of GFAP was also observed in mice non-tumoral neural stem cells indicating that this process occurs across species and is not restricted to cancerous cells. Immunofluorescence and videomicroscopy were used to capture these rare and transient events. Considering the role of intermediate filaments in cytoplasm organization and cell signaling, we propose that asymmetric distribution of GFAP could possibly participate in the regulation of normal and cancerous neural stem cell fate.

Origin of Asymmetric Charge Partitioning in the Dissociation of Gas-Phase Protein Homodimers

OpenAIRE

Jurchen, John C.; Williams, Evan R.

2003-01-01

The origin of asymmetric charge and mass partitioning observed for gas-phase dissociation of multiply charged macromolecular complexes has been hotly debated. These experiments hold the potential to provide detailed information about the interactions between the macromolecules within the complex. Here, this unusual phenomenon of asymmetric charge partitioning is investigated for several protein homodimers. Asymmetric charge partitioning in these ions depends on a number of factors, including ...

Activation of apurinic/apyrimidinic endonuclease in human cells by reactive oxygen species and its correlation with their adaptive response to genotoxicity of free radicals

OpenAIRE

Ramana, Chilakamarti V.; Boldogh, Istvan; Izumi, Tadahide; Mitra, Sankar

1998-01-01

Apurinic/apyrimidinic (AP) endonuclease (APE; EC 4.2.99.18) plays a central role in repair of DNA damage due to reactive oxygen species (ROS) because its DNA 3′-phosphoesterase activity removes 3′ blocking groups in DNA that are generated by DNA glycosylase/AP-lyases during removal of oxidized bases and by direct ROS reaction with DNA. The major human APE (APE-1) gene is activated selectively by sublethal levels of a variety of ROS and ROS generators, including ionizing radiation, but not by ...

Asymmetric cell division of stem cells in the lung and other systems

Directory of Open Access Journals (Sweden)

Mohamed eBerika

2014-07-01

Full Text Available New insights have been added to identification, behavior and cellular properties of embryonic and tissue-specific stem cells over the last few years. The modes of stem cell division, asymmetric versus symmetric, are tightly regulated during development and regeneration. The proper choice of a stem cell to divide asymmetrically or symmetrically has great consequences for development and disease because inappropriate asymmetric division disrupts organ morphogenesis, whereas uncontrolled symmetric division induces tumorigenesis. Therefore, understanding the behavior of lung stem cells could identify innovative solutions for restoring normal morphogenesis and/or regeneration of different organs. In this concise review, we describe recent studies in our laboratory about the mode of division of lung epithelial stem cells. We also compare asymmetric cell division in the lung stem cells with other tissues in different organisms.

Asymmetric Aminalization via Cation-Binding Catalysis

DEFF Research Database (Denmark)

Park, Sang Yeon; Liu, Yidong; Oh, Joong Suk

2018-01-01

Asymmetric cation-binding catalysis, in principle, can generate "chiral" anionic nucleophiles, where the counter cations are coordinated within chiral environments. Nitrogen-nucleophiles are intrinsically basic, therefore, its use as nucleophiles is often challenging and limiting the scope of the...

Uniform versus asymmetric shading mediates crown recession in conifers.

Directory of Open Access Journals (Sweden)

Amanda L Schoonmaker

Full Text Available In this study we explore the impact of asymmetrical vs. uniform crown shading on the mortality and growth of upper and lower branches within tree crowns, for two conifer species: shade intolerant lodgepole pine (Pinus contorta and shade tolerant white spruce (Picea glauca. We also explore xylem hydraulics, foliar nutrition, and carbohydrate status as drivers for growth and expansion of the lower and upper branches in various types of shading. This study was conducted over a two-year period across 10 regenerating forest sites dominated by lodgepole pine and white spruce, in the lower foothills of Alberta, Canada. Trees were assigned to one of four shading treatments: (1, complete uniform shading of the entire tree, (2 light asymmetric shading where the lower 1/4-1/3 of the tree crown was shaded, (3 heavy asymmetric shading as in (2 except with greater light reduction and (4 control in which no artificial shading occurred and most of the entire crown was exposed to full light. Asymmetrical shading of only the lower crown had a larger negative impact on the bud expansion and growth than did uniform shading, and the effect was stronger in pine relative to spruce. In addition, lower branches in pine also had lower carbon reserves, and reduced xylem-area specific conductivity compared to spruce. For both species, but particularly the pine, the needles of lower branches tended to store less C than upper branches in the asymmetric shade, which could suggest a movement of reserves away from the lower branches. The implications of these findings correspond with the inherent shade tolerance and self-pruning behavior of these conifers and supports a carbon based mechanism for branch mortality--mediated by an asymmetry in light exposure of the crown.

Diradical character dependences of the first and second hyperpolarizabilities of asymmetric open-shell singlet systems.

Science.gov (United States)

Nakano, Masayoshi; Champagne, Benoît

2013-06-28

The static first and second hyperpolarizabilities (referred to as β and γ, respectively) of asymmetric open-shell singlet systems have been investigated using the asymmetric two-site diradical model within the valence configuration interaction level of theory in order to reveal the effect of the asymmetric electron distribution on the diradical character and subsequently on β and γ. It is found that the increase of the asymmetric electron distribution causes remarkable changes in the amplitude and the sign of β and γ, and that their variations are intensified with the increase of the diradical character. These results demonstrate that the asymmetric open-shell singlet systems with intermediate diradical characters can exhibit further enhancements of β and γ as compared to conventional asymmetric closed-shell systems and also to symmetric open-shell singlet systems with intermediate diradical characters.

Substantial differences in bias between single-digest and double-digest RAD-seq libraries: A case study.

Science.gov (United States)

Flanagan, Sarah P; Jones, Adam G

2018-03-01

The trade-offs of using single-digest vs. double-digest restriction site-associated DNA sequencing (RAD-seq) protocols have been widely discussed. However, no direct empirical comparisons of the two methods have been conducted. Here, we sampled a single population of Gulf pipefish (Syngnathus scovelli) and genotyped 444 individuals using RAD-seq. Sixty individuals were subjected to single-digest RAD-seq (sdRAD-seq), and the remaining 384 individuals were genotyped using a double-digest RAD-seq (ddRAD-seq) protocol. We analysed the resulting Illumina sequencing data and compared the two genotyping methods when reads were analysed either together or separately. Coverage statistics, observed heterozygosity, and allele frequencies differed significantly between the two protocols, as did the results of selection components analysis. We also performed an in silico digestion of the Gulf pipefish genome and modelled five major sources of bias: PCR duplicates, polymorphic restriction sites, shearing bias, asymmetric sampling (i.e., genotyping fewer individuals with sdRAD-seq than with ddRAD-seq) and higher major allele frequencies. This combination of approaches allowed us to determine that polymorphic restriction sites, an asymmetric sampling scheme, mean allele frequencies and to some extent PCR duplicates all contribute to different estimates of allele frequencies between samples genotyped using sdRAD-seq versus ddRAD-seq. Our finding that sdRAD-seq and ddRAD-seq can result in different allele frequencies has implications for comparisons across studies and techniques that endeavour to identify genomewide signatures of evolutionary processes in natural populations. © 2017 John Wiley & Sons Ltd.

An efficient catalyst for asymmetric Reformatsky reaction

Indian Academy of Sciences (India)

rate enantioselectivity using N,N-dialkylnorephedrines as chiral ligands. ..... temperatures also, there was no product conversion. ... Optimization of reaction conditions for asymmetric Reformatsky reaction between benzaldehyde and α-.

A Novel Double-Piston Magnetorheological Damper for Space Truss Structures Vibration Suppression

Directory of Open Access Journals (Sweden)

Qiang Wang

2014-01-01

Full Text Available The design, fabrication, and testing of a new double-piston MR damper for space applications are discussed. The design concept for the damper is described in detail. The electromagnetic analysis of the design and the fabrication of the MR damper are also presented. The design analysis shows that the damper meets the weight and size requirements for being included in a space truss structure. The prototype design is tested in a damper dynamometer. The test results show that the damper can provide nearly 80 N of damping force at its maximum velocity and current. The test results also show that the seal drag could contribute significantly to the damping forces. Additionally, the test results indicate that both the work by the damper and damping force increase rapidly with increasing current at lower currents and taper off at higher currents as the damper starts to saturate. The damper force versus velocity plots show hysteresis in both pre- and postyield regions and asymmetric forces in jounce and rebound. A model is proposed for representing the force-displacement, force-velocity, and asymmetric forces observed in test results. A comparison of the modeling results and test data indicates that the model accurately represents the force characteristics of the damper.

LG tools for asymmetric wargaming

Science.gov (United States)

Stilman, Boris; Yakhnis, Alex; Yakhnis, Vladimir

2002-07-01

Asymmetric operations represent conflict where one of the sides would apply military power to influence the political and civil environment, to facilitate diplomacy, and to interrupt specified illegal activities. This is a special type of conflict where the participants do not initiate full-scale war. Instead, the sides may be engaged in a limited open conflict or one or several sides may covertly engage another side using unconventional or less conventional methods of engagement. They may include peace operations, combating terrorism, counterdrug operations, arms control, support of insurgencies or counterinsurgencies, show of force. An asymmetric conflict can be represented as several concurrent interlinked games of various kinds: military, transportation, economic, political, etc. Thus, various actions of peace violators, terrorists, drug traffickers, etc., can be expressed via moves in different interlinked games. LG tools allow us to fully capture the specificity of asymmetric conflicts employing the major LG concept of hypergame. Hypergame allows modeling concurrent interlinked processes taking place in geographically remote locations at different levels of resolution and time scale. For example, it allows us to model an antiterrorist operation taking place simultaneously in a number of countries around the globe and involving wide range of entities from individuals to combat units to governments. Additionally, LG allows us to model all sides of the conflict at their level of sophistication. Intelligent stakeholders are represented by means of LG generated intelligent strategies. TO generate those strategies, in addition to its own mathematical intelligence, the LG algorithm may incorporate the intelligence of the top-level experts in the respective problem domains. LG models the individual differences between intelligent stakeholders. The LG tools make it possible to incorporate most of the known traits of a stakeholder, i.e., real personalities involved in

Incompressibility of asymmetric nuclear matter

International Nuclear Information System (INIS)

Chen, Liewen; Cai, Baojun; Shen, Chun; Ko, Cheming; Xu, Jun; Li, Baoan

2010-01-01

Using an isospin- and momentum-dependent modified Gogny (MDI) interaction, the Skyrme-Hartree-Fock (SHF) approach, and a phenomenological modified Skyrme-like (MSL) model, we have studied the incompressibility K sat (δ) of isospin asymmetric nuclear matter at its saturation density. Our results show that in the expansion of K sat (δ) in powers of isospin asymmetry δ, i.e., K sat (δ) = K 0 + K sat,2 δ 2 + K sat,4 δ 4 + O(δ 6 ), the magnitude of the 4th-order K sat,4 parameter is generally small. The 2nd-order K sat,2 parameter thus essentially characterizes the isospin dependence of the incompressibility of asymmetric nuclear matter at saturation density. Furthermore, the K sat,2 can be expressed as K sat,2 = K sym – 6L – J 0 /K 0 L in terms of the slope parameter L and the curvature parameter K sym of the symmetry energy and the third-order derivative parameter J 0 of the energy of symmetric nuclear matter at saturation density, and we find the higher order J 0 contribution to K sat,2 generally cannot be neglected. Also, we have found a linear correlation between K sym and L as well as between J 0 /K 0 and K 0 . Using these correlations together with the empirical constraints on K 0 and L, the nuclear symmetry energy E sym (ρ0) at normal nuclear density, and the nucleon effective mass, we have obtained an estimated value of K sat,2 = -370 ± 120 MeV for the 2nd-order parameter in the isospin asymmetry expansion of the incompressibility of asymmetric nuclear matter at its saturation density. (author)

Treatment outcome of bimaxillary surgery for asymmetric skeletal class II deformity.

Science.gov (United States)

Chen, Yun-Fang; Liao, Yu-Fang; Chen, Yin-An; Chen, Yu-Ray

2018-05-04

Facial asymmetry is one of the main concerns in patients with a dentofacial deformity. The aims of the study were to (1) evaluate the changes in facial asymmetry after bimaxillary surgery for asymmetric skeletal class II deformity and (2) compare preoperative and postoperative facial asymmetry of class II patients with normal controls. The facial asymmetry was assessed for 30 adults (21 women and 9 men, mean age: 29.3 years) who consecutively underwent bimaxillary surgery for asymmetric skeletal class II deformity using cone-beam computed tomography before and at least 6 months after surgery. Thirty soft tissue and two dental landmarks were identified on each three-dimensional facial image, and the asymmetry index of each landmark was calculated. Results were compared with those of 30 normal control subjects (21 women and 9 men, mean age: 26.2 years) with skeletal class I structure. Six months after surgery, the asymmetric index of the lower face and total face decreased significantly (17.8 ± 29.4 and 16.6 ± 29.5 mm, respectively, both p class II patients had residual chin asymmetry. The postoperative total face asymmetric index was positively correlated with the preoperative asymmetric index (r = 0.37, p class II deformity resulted in a significant improvement in lower face asymmetry. However, approximately 50% of the patients still had residual chin asymmetry. The total face postoperative asymmetry was moderately related to the initial severity of asymmetry. These findings could help clinicians better understand orthognathic outcomes on different facial regions for patients with asymmetric class II deformity.

One-tube loop-mediated isothermal amplification combined with restriction endonuclease digestion and ELISA for colorimetric detection of resistance to isoniazid, ethambutol and streptomycin in Mycobacterium tuberculosis isolates.

Science.gov (United States)

Lee, Mei-Feng; Chen, Yen-Hsu; Hsu, Hui-Jine; Peng, Chien-Fang

2010-10-01

In this study, we designed a simple and rapid colorimetric detection method, a one-tube loop-mediated isothermal amplification (LAMP)-PCR-hybridization-restriction endonuclease-ELISA [one-tube LAMP-PCR-HY-RE-ELISA] system, to detect resistance to isoniazid, ethambutol and streptomycin in strains of Mycobacterium tuberculosis isolated from clinical specimens. The clinical performance of this method for detecting isoniazid-resistant, ethambutol-resistant and streptomycin-resistant isolates of M. tuberculosis showed 98.9%, 94.3% and 93.8%, respectively. This assay is rapid and convenient that can be performed within one working day. One-tube LAMP-PCR-HY-RE-ELISA system was designed based on hot spot point mutations in target drug-resistant genes, using LAMP-PCR, hybridization, digestion with restriction endonuclease and colorimetric method of ELISA. In this study, LAMP assay was used to amplify DNA from drug-resistant M. tuberculosis, and ELISA was used for colorimetrical determination. This assay will be a useful tool for rapid diagnosis of mutant codons in strains of M. tuberculosis for isoniazid at katG 315 and katG 463, ethambutol at embB 306 and embB 497, and streptomycin at rpsL 43. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

The Impacts of Dry Dynamic Cores on Asymmetric Hurricane Intensification

Science.gov (United States)

Guimond, Stephen R.; Reisner, Jon M.; Marras, Simone; Giraldo, Francis X.

2016-01-01

The fundamental pathways for tropical cyclone (TC) intensification are explored by considering axisymmetric and asymmetric impulsive thermal perturbations to balanced, TC-like vortices using the dynamic cores of three different nonlinear numerical models. Attempts at reproducing the results of previous work, which used the community WRF Model, revealed a discrepancy with the impacts of purely asymmetric thermal forcing. The current study finds that thermal asymmetries can have an important, largely positive role on the vortex intensification, whereas other studies find that asymmetric impacts are negligible. Analysis of the spectral energetics of each numerical model indicates that the vortex response to asymmetric thermal perturbations is significantly damped in WRF relative to the other models. Spectral kinetic energy budgets show that this anomalous damping is primarily due to the increased removal of kinetic energy from the vertical divergence of the vertical pressure flux, which is related to the flux of inertia-gravity wave energy. The increased kinetic energy in the other two models is shown to originate around the scales of the heating and propagate upscale with time from nonlinear effects. For very large thermal amplitudes (50 K), the anomalous removal of kinetic energy due to inertia-gravity wave activity is much smaller, resulting in good agreement between models. The results of this paper indicate that the numerical treatment of small-scale processes that project strongly onto inertia-gravity wave energy can lead to significant differences in asymmetric TC intensification. Sensitivity tests with different time integration schemes suggest that diffusion entering into the implicit solution procedure is partly responsible for the anomalous damping of energy.

High power CW output from low confinement asymmetric structure diode laser

NARCIS (Netherlands)

Iordache, G.; Buda, M.; Acket, G.A.; Roer, van de T.G.; Kaufmann, L.M.F.; Karouta, F.; Jagadish, C.; Tan, H.H.

1999-01-01

High power continuous wave output from diode lasers using low loss, low confinement, asymmetric structures is demonstrated. An asymmetric structure with an optical trap layer was grown by metal organic vapour phase epitaxy. Gain guided 50 µm wide stripe 1-3 mm long diode lasers were studied. 1.8 W